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Fluorine in PDB 1xdc: Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine

Enzymatic activity of Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine

All present enzymatic activity of Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine:
1.15.1.1;

Protein crystallography data

The structure of Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine, PDB code: 1xdc was solved by I.Ayala, J.J.Perry, J.Szczepanski, D.E.Cabelli, J.A.Tainer, M.T.Vala, H.S.Nick, D.N.Silverman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.60 / 1.85
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.036, 75.419, 67.818, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 25.2

Other elements in 1xdc:

The structure of Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Fluorine atom in the Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine (pdb code 1xdc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 15 binding sites of Fluorine where determined in the Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine, PDB code: 1xdc:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 15 in 1xdc

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Fluorine binding site 1 out of 15 in the Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F11

b:47.6
occ:0.70
 F A:YOF11 0.0 47.6 0.7
CE1 A:YOF11 1.3 46.9 1.0
CZ A:YOF11 2.3 46.5 1.0
CD1 A:YOF11 2.4 47.2 1.0
OH A:YOF11 2.7 45.6 1.0
CE2 A:YOF11 3.6 47.2 1.0
CG A:YOF11 3.7 47.4 1.0
CG A:GLN24 3.7 41.5 1.0
CD2 A:YOF11 4.1 46.2 1.0
NE2 A:GLN24 4.1 45.0 1.0
CD A:GLN24 4.4 44.9 1.0
CB A:SER28 4.6 35.0 1.0
CB A:GLN24 4.7 37.3 1.0
OG A:SER28 4.8 37.9 1.0
CA A:GLN24 4.8 35.7 1.0
CB A:YOF11 4.9 47.1 1.0

Fluorine binding site 2 out of 15 in 1xdc

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Fluorine binding site 2 out of 15 in the Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F34

b:23.2
occ:0.70
 F A:YOF34 0.0 23.2 0.7
CE1 A:YOF34 1.3 25.4 1.0
CZ A:YOF34 2.4 26.1 1.0
CD1 A:YOF34 2.4 25.4 1.0
OH A:YOF34 2.7 28.4 1.0
CE1 A:HIS74 3.0 22.3 1.0
O A:HOH665 3.3 36.3 1.0
NE2 A:HIS74 3.3 25.4 1.0
NE2 A:GLN143 3.5 26.0 1.0
CE2 A:YOF34 3.6 25.8 1.0
CB A:HIS30 3.6 29.0 1.0
CG A:YOF34 3.6 27.6 1.0
O A:HOH689 3.7 28.4 1.0
O A:HIS30 3.8 26.9 1.0
ND1 A:HIS74 3.8 28.1 1.0
C A:HIS30 3.9 27.6 1.0
CE1 A:HIS163 4.0 25.2 1.0
CD2 A:YOF34 4.1 26.9 1.0
MN A:MN500 4.2 26.8 1.0
CA A:HIS30 4.2 29.0 1.0
O A:HOH697 4.2 27.2 1.0
CD2 A:HIS74 4.3 25.9 1.0
N A:HIS31 4.3 27.7 1.0
NE2 A:HIS163 4.4 24.8 1.0
CD A:GLN143 4.4 23.5 1.0
CG A:HIS30 4.4 28.1 1.0
ND1 A:HIS30 4.5 28.8 1.0
CG A:HIS74 4.6 24.9 1.0
CA A:HIS31 4.8 26.7 1.0
CB A:YOF34 4.9 27.0 1.0

Fluorine binding site 3 out of 15 in 1xdc

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Fluorine binding site 3 out of 15 in the Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F45

b:36.8
occ:0.70
 F A:YOF45 0.0 36.8 0.7
CE1 A:YOF45 1.3 37.2 1.0
CD1 A:YOF45 2.4 36.8 1.0
CZ A:YOF45 2.4 37.3 1.0
OH A:YOF45 2.7 37.6 1.0
NE2 A:GLN57 3.1 29.6 1.0
CD1 A:LEU49 3.2 40.5 1.0
CD2 A:LEU49 3.4 40.5 1.0
CG A:LEU49 3.6 41.6 1.0
CB A:LEU49 3.6 39.3 1.0
CE2 A:YOF45 3.6 36.9 1.0
CG A:YOF45 3.6 36.6 1.0
CD A:GLN57 3.9 32.4 1.0
CD2 A:YOF45 4.1 36.5 1.0
CG A:GLN57 4.3 31.0 1.0
CA A:LEU49 4.5 39.7 1.0
O A:YOF45 4.5 39.8 1.0
OE1 A:GLN57 4.7 34.9 1.0
CB A:GLN57 4.9 28.6 1.0
CB A:YOF45 4.9 35.9 1.0
N A:LEU49 4.9 36.6 1.0

Fluorine binding site 4 out of 15 in 1xdc

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Fluorine binding site 4 out of 15 in the Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F165

b:28.3
occ:0.70
 F A:YOF165 0.0 28.3 0.7
CE1 A:YOF165 1.3 27.4 1.0
CZ A:YOF165 2.3 27.4 1.0
CD1 A:YOF165 2.4 26.2 1.0
OH A:YOF165 2.7 26.9 1.0
O A:VAL160 2.7 22.6 1.0
C A:VAL160 3.0 24.3 1.0
CA A:VAL160 3.2 22.4 1.0
O A:TRP161 3.2 25.3 1.0
NE A:ARG173 3.4 30.6 1.0
CE2 A:YOF165 3.6 27.6 1.0
C A:TRP161 3.6 25.2 1.0
CB A:VAL160 3.7 22.0 1.0
CG A:YOF165 3.7 26.7 1.0
CG A:ARG173 3.7 31.5 1.0
N A:TRP161 3.8 23.3 1.0
CD A:ARG173 3.9 32.1 1.0
N A:GLU162 4.1 24.7 1.0
CD2 A:YOF165 4.1 26.6 1.0
CZ A:ARG173 4.1 34.0 1.0
CA A:GLU162 4.2 25.1 1.0
CG1 A:VAL160 4.2 20.0 1.0
O A:HOH691 4.3 27.3 1.0
CA A:TRP161 4.3 24.5 1.0
NH2 A:ARG173 4.4 31.1 1.0
O A:ASP159 4.5 26.7 1.0
N A:VAL160 4.6 24.1 1.0
CD2 A:YOF176 4.6 32.4 1.0
CB A:ARG173 4.6 32.6 1.0
CE2 A:YOF176 4.6 32.1 1.0
CB A:YOF165 4.9 27.6 1.0
C A:ASP159 5.0 25.6 1.0

Fluorine binding site 5 out of 15 in 1xdc

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Fluorine binding site 5 out of 15 in the Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F166

b:28.8
occ:0.70
 F A:YOF166 0.0 28.8 0.7
CE1 A:YOF166 1.3 26.6 1.0
CD1 A:YOF166 2.3 26.4 1.0
CZ A:YOF166 2.4 26.7 1.0
NE2 B:HIS30 2.8 23.0 1.0
OH A:YOF166 2.9 26.8 1.0
CE1 B:HIS30 2.9 25.1 1.0
CA A:ASN171 3.2 31.9 1.0
O A:HOH563 3.3 33.8 1.0
N A:ASN171 3.4 31.5 1.0
O A:LYS170 3.5 31.4 1.0
C A:LYS170 3.5 31.2 1.0
CB A:ASN171 3.6 32.0 1.0
CG A:YOF166 3.6 25.9 1.0
OE2 A:GLU162 3.7 22.8 1.0
CE2 A:YOF166 3.7 26.1 1.0
CB B:HIS163 3.7 21.2 1.0
CD2 A:YOF166 4.1 27.1 1.0
CD2 B:HIS30 4.2 23.5 1.0
ND1 B:HIS30 4.3 25.0 1.0
CD A:GLU162 4.4 21.7 1.0
CA A:LYS170 4.5 32.2 1.0
C A:ASN171 4.5 32.3 1.0
CG B:HIS163 4.6 22.4 1.0
CB A:YOF166 4.8 26.5 1.0
CA B:HIS163 4.8 22.6 1.0
O A:HOH587 4.8 39.1 1.0
CE2 A:YOF165 4.8 27.6 1.0
CG A:GLU162 4.9 22.6 1.0
ND1 B:HIS163 4.9 21.0 1.0
CG B:HIS30 4.9 22.6 1.0
CG A:ASN171 4.9 34.9 1.0
O A:ASN171 4.9 31.8 1.0

Fluorine binding site 6 out of 15 in 1xdc

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Fluorine binding site 6 out of 15 in the Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F169

b:34.4
occ:0.70
 F A:YOF169 0.0 34.4 0.7
CE1 A:YOF169 1.3 34.8 1.0
CZ A:YOF169 2.3 35.5 1.0
CD1 A:YOF169 2.4 33.2 1.0
OH A:YOF169 2.7 37.0 1.0
O A:HOH582 3.5 42.6 1.0
CE2 A:YOF169 3.6 35.1 1.0
O A:ASP175 3.6 36.3 1.0
CG A:YOF169 3.7 32.7 1.0
CB A:ALA179 3.9 38.6 1.0
C A:ASP175 4.0 36.4 1.0
CB A:ASP175 4.1 39.1 1.0
CD2 A:YOF169 4.1 33.2 1.0
NE2 A:GLN168 4.2 34.6 1.0
N A:YOF176 4.5 35.4 1.0
CA A:ASP175 4.6 36.3 1.0
CA A:YOF176 4.7 34.6 1.0
CB A:YOF169 4.9 31.6 1.0

Fluorine binding site 7 out of 15 in 1xdc

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Fluorine binding site 7 out of 15 in the Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F176

b:32.9
occ:0.70
 F A:YOF176 0.0 32.9 0.7
CE1 A:YOF176 1.3 31.8 1.0
CZ A:YOF176 2.3 30.3 1.0
CD1 A:YOF176 2.4 32.2 1.0
OH A:YOF176 2.7 28.1 1.0
O A:HOH652 2.8 29.5 1.0
CD1 A:ILE18 3.3 35.7 1.0
CE2 A:YOF176 3.6 32.1 1.0
CG A:YOF176 3.7 32.7 1.0
O A:ALA164 3.7 26.4 1.0
CG1 A:ILE18 3.7 38.5 1.0
CD1 A:ILE180 3.9 34.6 1.0
CD2 A:YOF176 4.1 32.4 1.0
CG1 A:ILE180 4.2 36.9 1.0
CB A:ILE180 4.3 35.4 1.0
CG2 A:ILE18 4.7 40.4 1.0
C A:ALA164 4.7 26.7 1.0
CZ A:PHE77 4.8 26.2 1.0
CB A:ILE18 4.9 39.6 1.0
O A:YOF176 4.9 33.0 1.0
CB A:YOF176 4.9 32.7 1.0

Fluorine binding site 8 out of 15 in 1xdc

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Fluorine binding site 8 out of 15 in the Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F193

b:42.5
occ:0.70
 F A:YOF193 0.0 42.5 0.7
CE1 A:YOF193 1.3 43.6 1.0
CD1 A:YOF193 2.4 42.8 1.0
CZ A:YOF193 2.4 43.8 1.0
OH A:YOF193 2.8 42.6 1.0
CE1 A:PHE128 3.3 32.6 1.0
CD1 A:PHE128 3.4 33.6 1.0
CD2 A:LEU135 3.5 31.7 1.0
CG A:YOF193 3.6 42.6 1.0
CE2 A:YOF193 3.6 44.1 1.0
CE A:LYS197 3.8 72.0 1.0
CB A:ALA96 3.9 37.2 1.0
CG A:LEU135 4.0 29.6 1.0
CD2 A:YOF193 4.1 43.8 1.0
CZ A:PHE128 4.6 33.5 1.0
CD A:LYS197 4.6 71.5 1.0
CG A:PHE128 4.6 30.4 1.0
CD1 A:LEU135 4.7 32.1 1.0
NH2 A:ARG99 4.7 51.3 1.0
CB A:YOF193 4.9 40.6 1.0
N A:LEU135 5.0 29.1 1.0

Fluorine binding site 9 out of 15 in 1xdc

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Fluorine binding site 9 out of 15 in the Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F9

b:30.5
occ:0.70
 F B:YOF9 0.0 30.5 0.7
CE1 B:YOF9 1.3 31.5 1.0
CD1 B:YOF9 2.3 31.0 1.0
CZ B:YOF9 2.4 31.6 1.0
OH B:YOF9 2.8 30.9 1.0
CE B:MET23 2.9 23.8 1.0
CD1 B:LEU7 3.6 32.9 1.0
CG B:YOF9 3.6 33.0 1.0
CE2 B:YOF9 3.6 33.0 1.0
CD1 B:LEU14 3.6 27.5 1.0
CG B:LEU14 3.9 26.7 1.0
CD2 B:YOF9 4.1 32.1 1.0
O B:ASP10 4.3 31.5 1.0
SD B:MET23 4.3 27.8 1.0
CG B:LEU7 4.4 33.8 1.0
CD2 B:LEU7 4.4 33.8 1.0
CB B:LEU7 4.4 33.8 1.0
O B:YOF9 4.6 34.5 1.0
CG B:MET23 4.6 25.2 1.0
CD2 B:LEU14 4.6 26.1 1.0
CB B:YOF9 4.9 33.0 1.0
CB B:MET23 5.0 27.4 1.0

Fluorine binding site 10 out of 15 in 1xdc

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Fluorine binding site 10 out of 15 in the Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3- Fluorotyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F34

b:20.8
occ:0.70
 F B:YOF34 0.0 20.8 0.7
CE1 B:YOF34 1.3 22.5 1.0
CZ B:YOF34 2.3 22.6 1.0
CD1 B:YOF34 2.4 21.7 1.0
OH B:YOF34 2.7 24.1 1.0
CE1 B:HIS74 3.2 19.1 1.0
O B:HOH806 3.2 25.2 1.0
NE2 B:HIS74 3.5 20.9 1.0
NE2 B:GLN143 3.6 17.7 1.0
CB B:HIS30 3.6 23.3 1.0
CE2 B:YOF34 3.6 23.5 1.0
O B:HOH704 3.7 34.4 1.0
CG B:YOF34 3.7 19.3 1.0
O B:HIS30 3.8 23.2 1.0
C B:HIS30 3.9 23.0 1.0
CE1 B:HIS163 3.9 22.2 1.0
ND1 B:HIS74 4.0 19.2 1.0
NE2 B:HIS163 4.1 20.7 1.0
CD2 B:YOF34 4.1 21.1 1.0
O B:HOH852 4.1 19.1 1.0
ND1 B:HIS30 4.1 25.0 1.0
MN B:MN600 4.2 21.5 1.0
CA B:HIS30 4.2 24.2 1.0
CG B:HIS30 4.3 22.6 1.0
N B:HIS31 4.4 21.5 1.0
CD2 B:HIS74 4.5 19.5 1.0
CD B:GLN143 4.5 18.4 1.0
CG B:HIS74 4.7 18.3 1.0
O B:HOH800 4.9 28.0 1.0
CA B:HIS31 4.9 21.8 1.0
CB B:YOF34 4.9 20.6 1.0
ND1 B:HIS163 5.0 21.0 1.0

Reference:

I.Ayala, J.J.Perry, J.Szczepanski, J.A.Tainer, M.T.Vala, H.S.Nick, D.N.Silverman. Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3-Fluorotyrosine Biophys.J. V. 89 4171 2005.
ISSN: ISSN 0006-3495
PubMed: 16150974
DOI: 10.1529/BIOPHYSJ.105.060616
Page generated: Wed Jul 31 13:17:17 2024

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