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Manganese in PDB 2p4k: Contribution to Structure and Catalysis of Tyrosine 34 in Human Manganese Superoxide Dismutase

Enzymatic activity of Contribution to Structure and Catalysis of Tyrosine 34 in Human Manganese Superoxide Dismutase

All present enzymatic activity of Contribution to Structure and Catalysis of Tyrosine 34 in Human Manganese Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of Contribution to Structure and Catalysis of Tyrosine 34 in Human Manganese Superoxide Dismutase, PDB code: 2p4k was solved by J.J.Perry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.20 / 1.48
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.559, 77.798, 136.097, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 22.2

Manganese Binding Sites:

The binding sites of Manganese atom in the Contribution to Structure and Catalysis of Tyrosine 34 in Human Manganese Superoxide Dismutase (pdb code 2p4k). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Contribution to Structure and Catalysis of Tyrosine 34 in Human Manganese Superoxide Dismutase, PDB code: 2p4k:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2p4k

Go back to Manganese Binding Sites List in 2p4k
Manganese binding site 1 out of 4 in the Contribution to Structure and Catalysis of Tyrosine 34 in Human Manganese Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Contribution to Structure and Catalysis of Tyrosine 34 in Human Manganese Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn199

b:5.6
occ:1.00
 OD2 A:ASP159 2.1 13.0 1.0
NE2 A:HIS163 2.2 11.7 1.0
NE2 A:HIS26 2.2 10.9 1.0
NE2 A:HIS74 2.2 13.3 1.0
O A:HOH511 2.3 13.5 1.0
CD2 A:HIS163 3.1 11.2 1.0
CG A:ASP159 3.1 11.5 1.0
CD2 A:HIS74 3.1 11.6 1.0
CD2 A:HIS26 3.2 12.1 1.0
CE1 A:HIS163 3.2 11.7 1.0
CE1 A:HIS26 3.2 9.6 1.0
CE1 A:HIS74 3.2 17.0 1.0
OD1 A:ASP159 3.5 13.0 1.0
ND1 A:HIS26 4.3 12.3 1.0
CZ2 A:TRP123 4.3 10.4 1.0
ND1 A:HIS163 4.3 12.1 1.0
CG A:HIS26 4.3 11.4 1.0
CG A:HIS163 4.3 11.8 1.0
NE2 A:GLN143 4.3 22.0 1.0
CG A:HIS74 4.3 12.9 1.0
ND1 A:HIS74 4.4 17.4 1.0
CB A:ASP159 4.4 10.2 1.0
CB A:TRP161 4.5 10.6 1.0
CG A:TRP161 4.6 13.0 1.0
CD1 A:TRP161 4.7 12.9 1.0
CH2 A:TRP123 4.9 9.7 1.0

Manganese binding site 2 out of 4 in 2p4k

Go back to Manganese Binding Sites List in 2p4k
Manganese binding site 2 out of 4 in the Contribution to Structure and Catalysis of Tyrosine 34 in Human Manganese Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Contribution to Structure and Catalysis of Tyrosine 34 in Human Manganese Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn199

b:5.1
occ:1.00
 OD2 B:ASP159 2.0 12.8 1.0
NE2 B:HIS163 2.2 10.2 1.0
NE2 B:HIS26 2.2 9.9 1.0
NE2 B:HIS74 2.2 11.2 1.0
O B:HOH528 2.3 16.8 1.0
CD2 B:HIS163 3.1 10.5 1.0
CG B:ASP159 3.1 11.6 1.0
CE1 B:HIS26 3.1 10.8 1.0
CD2 B:HIS74 3.2 10.6 1.0
CE1 B:HIS163 3.2 10.9 1.0
CD2 B:HIS26 3.2 9.7 1.0
CE1 B:HIS74 3.2 13.0 1.0
OD1 B:ASP159 3.5 14.3 1.0
ND1 B:HIS163 4.3 11.8 1.0
CG B:HIS163 4.3 10.5 1.0
ND1 B:HIS26 4.3 11.9 1.0
CZ2 B:TRP123 4.3 9.9 1.0
ND1 B:HIS74 4.3 15.1 1.0
CG B:HIS26 4.3 11.1 1.0
CG B:HIS74 4.3 11.3 1.0
CB B:ASP159 4.4 10.3 1.0
NE2 B:GLN143 4.4 22.0 1.0
CB B:TRP161 4.6 11.4 1.0
CG B:TRP161 4.7 10.3 1.0
CD1 B:TRP161 4.8 11.9 1.0
CH2 B:TRP123 4.9 10.6 1.0
CB B:ALA164 5.0 11.6 1.0

Manganese binding site 3 out of 4 in 2p4k

Go back to Manganese Binding Sites List in 2p4k
Manganese binding site 3 out of 4 in the Contribution to Structure and Catalysis of Tyrosine 34 in Human Manganese Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Contribution to Structure and Catalysis of Tyrosine 34 in Human Manganese Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn199

b:6.2
occ:1.00
 OD2 C:ASP159 2.0 13.3 1.0
NE2 C:HIS163 2.2 10.4 1.0
NE2 C:HIS74 2.2 12.0 1.0
NE2 C:HIS26 2.2 11.5 1.0
O C:HOH465 2.3 15.3 1.0
CD2 C:HIS163 3.1 11.6 1.0
CG C:ASP159 3.1 10.7 1.0
CD2 C:HIS74 3.1 11.4 1.0
CE1 C:HIS26 3.1 11.3 1.0
CE1 C:HIS163 3.2 12.1 1.0
CD2 C:HIS26 3.2 12.1 1.0
CE1 C:HIS74 3.3 15.3 1.0
OD1 C:ASP159 3.5 13.3 1.0
NE2 C:GLN143 4.3 22.1 1.0
ND1 C:HIS26 4.3 12.3 1.0
CZ2 C:TRP123 4.3 11.8 1.0
ND1 C:HIS163 4.3 13.3 1.0
CG C:HIS163 4.3 11.8 1.0
CG C:HIS74 4.3 13.1 1.0
CG C:HIS26 4.3 12.6 1.0
ND1 C:HIS74 4.4 17.6 1.0
CB C:ASP159 4.4 11.6 1.0
CB C:TRP161 4.5 11.0 1.0
CG C:TRP161 4.6 12.0 1.0
CD1 C:TRP161 4.8 11.7 1.0
CH2 C:TRP123 4.9 12.3 1.0
O C:HOH303 4.9 36.9 1.0

Manganese binding site 4 out of 4 in 2p4k

Go back to Manganese Binding Sites List in 2p4k
Manganese binding site 4 out of 4 in the Contribution to Structure and Catalysis of Tyrosine 34 in Human Manganese Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Contribution to Structure and Catalysis of Tyrosine 34 in Human Manganese Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn199

b:6.2
occ:1.00
 OD2 D:ASP159 2.1 12.2 1.0
NE2 D:HIS163 2.2 10.5 1.0
NE2 D:HIS74 2.2 13.9 1.0
NE2 D:HIS26 2.2 12.0 1.0
O D:HOH494 2.3 17.3 1.0
CG D:ASP159 3.1 10.1 1.0
CD2 D:HIS163 3.1 10.8 1.0
CD2 D:HIS74 3.2 11.7 1.0
CE1 D:HIS163 3.2 12.0 1.0
CE1 D:HIS74 3.2 14.3 1.0
CE1 D:HIS26 3.2 11.4 1.0
CD2 D:HIS26 3.2 10.8 1.0
OD1 D:ASP159 3.4 14.2 1.0
ND1 D:HIS163 4.3 12.3 1.0
ND1 D:HIS74 4.3 14.5 1.0
CG D:HIS163 4.3 11.3 1.0
ND1 D:HIS26 4.3 12.1 1.0
CG D:HIS74 4.3 12.0 1.0
CZ2 D:TRP123 4.3 13.5 1.0
CG D:HIS26 4.4 11.9 1.0
NE2 D:GLN143 4.4 18.2 1.0
CB D:ASP159 4.4 10.3 1.0
CB D:TRP161 4.6 11.5 1.0
CG D:TRP161 4.6 12.6 1.0
CD1 D:TRP161 4.8 10.9 1.0
CH2 D:TRP123 4.9 13.2 1.0

Reference:

J.J.Perry, A.S.Hearn, D.E.Cabelli, H.S.Nick, J.A.Tainer, D.N.Silverman. Contribution of Human Manganese Superoxide Dismutase Tyrosine 34 to Structure and Catalysis. Biochemistry V. 48 3417 2009.
ISSN: ISSN 0006-2960
PubMed: 19265433
DOI: 10.1021/BI8023288
Page generated: Sat Oct 5 14:49:56 2024

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