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Manganese in PDB 2gds: Interrupting the Hydrogen Bonding Network at the Active Site of Human Manganese Superoxide Dismutase

Enzymatic activity of Interrupting the Hydrogen Bonding Network at the Active Site of Human Manganese Superoxide Dismutase

All present enzymatic activity of Interrupting the Hydrogen Bonding Network at the Active Site of Human Manganese Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of Interrupting the Hydrogen Bonding Network at the Active Site of Human Manganese Superoxide Dismutase, PDB code: 2gds 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) N/A / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.700, 77.570, 135.460, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 30

Manganese Binding Sites:

The binding sites of Manganese atom in the Interrupting the Hydrogen Bonding Network at the Active Site of Human Manganese Superoxide Dismutase (pdb code 2gds). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Interrupting the Hydrogen Bonding Network at the Active Site of Human Manganese Superoxide Dismutase, PDB code: 2gds:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2gds

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Manganese binding site 1 out of 4 in the Interrupting the Hydrogen Bonding Network at the Active Site of 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 Interrupting the Hydrogen Bonding Network at the Active Site of Human Manganese Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn199

b:16.1
occ:1.00
 O A:HOH5011 2.0 17.1 1.0
OD1 A:ASP159 2.0 15.2 1.0
NE2 A:HIS163 2.1 2.0 1.0
NE2 A:HIS74 2.2 22.3 1.0
NE2 A:HIS26 2.2 18.9 1.0
CE1 A:HIS163 3.0 9.4 1.0
CG A:ASP159 3.0 17.5 1.0
CE1 A:HIS74 3.1 20.2 1.0
CD2 A:HIS163 3.1 7.6 1.0
CE1 A:HIS26 3.2 13.2 1.0
CD2 A:HIS26 3.2 14.1 1.0
CD2 A:HIS74 3.3 16.9 1.0
OD2 A:ASP159 3.4 14.5 1.0
ND1 A:HIS163 4.1 10.2 1.0
NE2 A:GLN143 4.2 15.4 1.0
ND1 A:HIS74 4.2 20.5 1.0
CG A:HIS163 4.2 12.5 1.0
ND1 A:HIS26 4.3 12.3 1.0
CB A:TRP161 4.3 12.5 1.0
CG A:HIS26 4.3 14.3 1.0
CB A:ASP159 4.3 6.3 1.0
CZ2 A:TRP123 4.4 10.3 1.0
CG A:HIS74 4.4 13.7 1.0
CG A:TRP161 4.5 11.9 1.0
CD1 A:TRP161 4.7 10.8 1.0
CB A:ALA164 4.9 11.2 1.0
CD2 A:TRP161 4.9 7.0 1.0

Manganese binding site 2 out of 4 in 2gds

Go back to Manganese Binding Sites List in 2gds
Manganese binding site 2 out of 4 in the Interrupting the Hydrogen Bonding Network at the Active Site of 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 Interrupting the Hydrogen Bonding Network at the Active Site of Human Manganese Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn200

b:24.9
occ:1.00
 OD1 B:ASP159 2.0 26.9 1.0
NE2 B:HIS163 2.1 6.5 1.0
NE2 B:HIS74 2.1 19.0 1.0
NE2 B:HIS26 2.2 30.1 1.0
O B:HOH5022 2.3 22.3 1.0
CE1 B:HIS74 3.0 17.6 1.0
O B:HOH945 3.0 59.0 1.0
CE1 B:HIS163 3.0 7.2 1.0
CG B:ASP159 3.1 20.5 1.0
CD2 B:HIS26 3.2 26.4 1.0
CE1 B:HIS26 3.2 27.2 1.0
CD2 B:HIS163 3.2 17.1 1.0
CD2 B:HIS74 3.3 13.6 1.0
OD2 B:ASP159 3.6 24.6 1.0
ND1 B:HIS74 4.2 16.0 1.0
ND1 B:HIS163 4.2 10.3 1.0
CG B:HIS163 4.3 15.1 1.0
ND1 B:HIS26 4.3 22.3 1.0
CB B:ASP159 4.3 21.0 1.0
CG B:HIS74 4.3 13.5 1.0
CG B:HIS26 4.3 25.4 1.0
NE2 B:GLN143 4.4 8.0 1.0
CZ2 B:TRP123 4.5 12.9 1.0
CB B:TRP161 4.5 12.5 1.0
CG B:TRP161 4.7 10.4 1.0
CB B:ALA164 4.7 12.7 1.0
CD1 B:TRP161 4.9 12.4 1.0
CH2 B:TRP123 4.9 15.1 1.0

Manganese binding site 3 out of 4 in 2gds

Go back to Manganese Binding Sites List in 2gds
Manganese binding site 3 out of 4 in the Interrupting the Hydrogen Bonding Network at the Active Site of 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 Interrupting the Hydrogen Bonding Network at the Active Site of Human Manganese Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn201

b:19.1
occ:1.00
 OD1 C:ASP159 2.0 21.4 1.0
NE2 C:HIS74 2.1 17.0 1.0
NE2 C:HIS163 2.1 13.9 1.0
NE2 C:HIS26 2.3 30.1 1.0
O C:HOH5033 2.3 22.6 1.0
CE1 C:HIS74 3.0 20.4 1.0
CG C:ASP159 3.0 16.4 1.0
CE1 C:HIS163 3.1 14.1 1.0
CD2 C:HIS163 3.1 19.4 1.0
CD2 C:HIS74 3.1 17.4 1.0
CE1 C:HIS26 3.2 25.7 1.0
CD2 C:HIS26 3.2 25.8 1.0
OD2 C:ASP159 3.4 17.2 1.0
ND1 C:HIS74 4.1 16.7 1.0
ND1 C:HIS163 4.2 7.6 1.0
CG C:HIS74 4.2 19.4 1.0
CG C:HIS163 4.2 16.1 1.0
CB C:ASP159 4.3 10.2 1.0
ND1 C:HIS26 4.3 21.3 1.0
CG C:HIS26 4.4 26.7 1.0
CZ2 C:TRP123 4.4 15.9 1.0
NE2 C:GLN143 4.5 5.0 1.0
CB C:TRP161 4.6 12.2 1.0
CG C:TRP161 4.7 14.2 1.0
CD1 C:TRP161 4.9 13.6 1.0
CH2 C:TRP123 5.0 20.6 1.0

Manganese binding site 4 out of 4 in 2gds

Go back to Manganese Binding Sites List in 2gds
Manganese binding site 4 out of 4 in the Interrupting the Hydrogen Bonding Network at the Active Site of 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 Interrupting the Hydrogen Bonding Network at the Active Site of Human Manganese Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn202

b:17.6
occ:1.00
 NE2 D:HIS163 2.0 11.9 1.0
O D:HOH5044 2.1 8.5 1.0
OD1 D:ASP159 2.1 12.3 1.0
NE2 D:HIS74 2.1 19.6 1.0
NE2 D:HIS26 2.2 19.0 1.0
CE1 D:HIS74 2.9 22.2 1.0
CD2 D:HIS163 3.0 13.2 1.0
CE1 D:HIS163 3.1 11.9 1.0
CE1 D:HIS26 3.2 15.1 1.0
CG D:ASP159 3.2 13.0 1.0
CD2 D:HIS26 3.2 15.2 1.0
CD2 D:HIS74 3.3 18.6 1.0
OD2 D:ASP159 3.6 26.0 1.0
ND1 D:HIS74 4.1 18.9 1.0
CG D:HIS163 4.1 16.3 1.0
ND1 D:HIS163 4.2 11.3 1.0
NE2 D:GLN143 4.2 15.1 1.0
CZ2 D:TRP123 4.3 3.9 1.0
ND1 D:HIS26 4.3 13.2 1.0
CG D:HIS74 4.3 20.7 1.0
CG D:HIS26 4.4 17.4 1.0
CB D:ASP159 4.4 10.4 1.0
CB D:TRP161 4.5 15.8 1.0
CG D:TRP161 4.6 18.0 1.0
CB D:ALA164 4.8 11.9 1.0
CD1 D:TRP161 4.9 6.9 1.0
CE2 D:TRP123 5.0 9.6 1.0
CH2 D:TRP123 5.0 4.4 1.0

Reference:

C.A.Ramilo, V.Leveque, Y.Guan, J.R.Lepock, J.A.Tainer, H.S.Nick, D.N.Silverman. Interrupting the Hydrogen Bond Network at the Active Site of Human Manganese Superoxide Dismutase J.Biol.Chem. V. 274 27711 1999.
ISSN: ISSN 0021-9258
PubMed: 10488113
DOI: 10.1074/JBC.274.39.27711
Page generated: Sat Oct 5 14:10:06 2024

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