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Zinc in PDB 4wnc: Crystal Structure of Human Wild-Type Gapdh at 1.99 Angstroms Resolution

Enzymatic activity of Crystal Structure of Human Wild-Type Gapdh at 1.99 Angstroms Resolution

All present enzymatic activity of Crystal Structure of Human Wild-Type Gapdh at 1.99 Angstroms Resolution:
1.2.1.12;

Protein crystallography data

The structure of Crystal Structure of Human Wild-Type Gapdh at 1.99 Angstroms Resolution, PDB code: 4wnc was solved by E.D.Garcin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.36 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 132.537, 81.423, 147.802, 90.00, 90.06, 90.00
R / Rfree (%) 13.9 / 17.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Wild-Type Gapdh at 1.99 Angstroms Resolution (pdb code 4wnc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Human Wild-Type Gapdh at 1.99 Angstroms Resolution, PDB code: 4wnc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4wnc

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Zinc binding site 1 out of 6 in the Crystal Structure of Human Wild-Type Gapdh at 1.99 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Wild-Type Gapdh at 1.99 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn402

b:19.1
occ:1.00
 OXT O:ACT403 1.9 17.6 1.0
OE1 E:GLU106 1.9 18.4 1.0
OD2 E:ASP127 1.9 17.2 1.0
NE2 O:HIS306 2.1 17.5 1.0
O O:ACT403 2.6 22.3 1.0
C O:ACT403 2.7 22.2 1.0
CD E:GLU106 2.7 33.2 1.0
OE2 E:GLU106 2.8 24.7 1.0
CG E:ASP127 3.1 21.9 1.0
CD2 O:HIS306 3.1 17.0 1.0
CE1 O:HIS306 3.1 18.2 1.0
HB E:THR104 3.2 23.4 1.0
HD2 O:HIS306 3.2 20.4 1.0
HE1 O:HIS306 3.3 21.9 1.0
HD3 O:PRO252 3.4 21.2 1.0
HB3 O:PRO252 3.6 23.2 1.0
HG3 O:PRO252 3.6 24.4 1.0
H E:GLU106 3.8 20.9 1.0
OD1 E:ASP127 3.8 16.9 1.0
HB3 E:ASP127 3.8 21.4 1.0
O O:HOH820 3.9 43.5 1.0
H E:MET105 3.9 17.7 1.0
CB E:ASP127 4.0 17.9 1.0
HB2 E:MET105 4.1 18.1 1.0
CH3 O:ACT403 4.1 30.0 1.0
CG E:GLU106 4.1 24.7 1.0
CB E:THR104 4.2 19.5 1.0
CD O:PRO252 4.2 17.7 1.0
CG O:PRO252 4.2 20.3 1.0
ND1 O:HIS306 4.2 16.8 1.0
CG O:HIS306 4.2 17.1 1.0
HB2 E:ASP127 4.2 21.4 1.0
CB O:PRO252 4.3 19.3 1.0
HG3 E:GLU106 4.4 29.6 1.0
H1 O:ACT403 4.4 36.0 1.0
HB2 E:GLU106 4.5 25.9 1.0
HG21 E:THR104 4.5 28.5 1.0
N E:MET105 4.5 14.7 1.0
HG22 E:THR104 4.5 28.5 1.0
N E:GLU106 4.6 17.4 1.0
H3 O:ACT403 4.6 36.0 1.0
CG2 E:THR104 4.7 23.7 1.0
H2 O:ACT403 4.7 36.0 1.0
HG2 E:GLU106 4.7 29.6 1.0
HG1 E:THR104 4.7 24.4 1.0
CB E:GLU106 4.8 21.6 1.0
HA E:THR104 4.8 18.6 1.0
N O:PRO252 4.9 16.6 1.0
OG1 E:THR104 4.9 20.3 1.0
O O:HOH819 4.9 36.3 1.0
HD2 O:PRO252 4.9 21.2 1.0
O E:HOH655 5.0 32.9 1.0
CB E:MET105 5.0 15.1 1.0
CA E:THR104 5.0 15.5 1.0

Zinc binding site 2 out of 6 in 4wnc

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Zinc binding site 2 out of 6 in the Crystal Structure of Human Wild-Type Gapdh at 1.99 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Wild-Type Gapdh at 1.99 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:44.4
occ:1.00
 OE1 A:GLU63 2.1 52.9 1.0
CD A:GLU63 2.8 50.8 1.0
OE2 A:GLU63 2.9 46.1 1.0
HZ1 A:LYS61 3.7 84.1 1.0
HZ3 A:LYS61 4.1 84.1 1.0
CG A:GLU63 4.3 33.4 1.0
NZ A:LYS61 4.3 70.1 1.0
HG3 A:GLU63 4.5 40.1 1.0
HG2 A:GLU63 4.7 40.1 1.0
HE3 A:LYS61 4.8 61.3 1.0
HZ2 A:LYS61 5.0 84.1 1.0

Zinc binding site 3 out of 6 in 4wnc

Go back to Zinc Binding Sites List in 4wnc
Zinc binding site 3 out of 6 in the Crystal Structure of Human Wild-Type Gapdh at 1.99 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human Wild-Type Gapdh at 1.99 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:28.8
occ:0.74
 OE1 B:GLU63 2.1 54.0 1.0
CD B:GLU63 2.8 55.9 1.0
OE2 B:GLU63 2.9 60.0 1.0
HZ2 B:LYS61 3.6 97.5 1.0
HZ1 B:LYS61 4.0 97.5 1.0
NZ B:LYS61 4.2 81.3 1.0
CG B:GLU63 4.3 39.9 1.0
HG3 B:GLU63 4.5 47.8 1.0
HG2 B:GLU63 4.7 47.8 1.0
HZ3 B:LYS61 4.8 97.5 1.0
HE3 B:LYS61 4.9 76.4 1.0

Zinc binding site 4 out of 6 in 4wnc

Go back to Zinc Binding Sites List in 4wnc
Zinc binding site 4 out of 6 in the Crystal Structure of Human Wild-Type Gapdh at 1.99 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Wild-Type Gapdh at 1.99 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:15.7
occ:0.86
 O C:HOH501 2.0 19.1 1.0
OXT C:GLU335 2.1 24.3 1.0
O C:HOH509 2.6 16.1 1.0
C C:GLU335 3.1 29.2 1.0
O C:GLU335 3.3 34.4 1.0
HB2 C:GLU335 4.0 33.2 1.0
O C:HOH527 4.2 30.5 1.0
CA C:GLU335 4.5 16.8 1.0
CB C:GLU335 4.7 27.6 1.0
O C:ALA332 4.8 15.2 1.0
HG3 C:GLU335 4.9 33.7 1.0
HA C:GLU335 5.0 20.2 1.0

Zinc binding site 5 out of 6 in 4wnc

Go back to Zinc Binding Sites List in 4wnc
Zinc binding site 5 out of 6 in the Crystal Structure of Human Wild-Type Gapdh at 1.99 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Human Wild-Type Gapdh at 1.99 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:19.6
occ:1.00
 O C:ACT404 1.9 14.7 1.0
OE1 C:GLU106 1.9 20.6 1.0
OD2 C:ASP127 2.0 18.9 1.0
CD C:GLU106 2.6 33.1 1.0
C C:ACT404 2.7 22.3 1.0
OXT C:ACT404 2.7 19.8 1.0
OE2 C:GLU106 2.7 27.6 1.0
CG C:ASP127 3.1 16.6 1.0
HB C:THR104 3.2 22.8 1.0
H C:GLU106 3.7 21.1 1.0
HB3 C:ASP127 3.8 22.9 1.0
OD1 C:ASP127 3.8 16.0 1.0
O C:HOH502 3.9 31.9 1.0
H C:MET105 3.9 17.9 1.0
CB C:ASP127 4.0 19.1 1.0
HB2 C:MET105 4.1 19.8 1.0
CG C:GLU106 4.1 25.6 1.0
CH3 C:ACT404 4.1 34.1 1.0
CB C:THR104 4.2 19.0 1.0
HB2 C:ASP127 4.2 22.9 1.0
HG3 C:GLU106 4.3 30.7 1.0
HB2 C:GLU106 4.5 26.6 1.0
H3 C:ACT404 4.5 40.9 1.0
N C:MET105 4.5 14.9 1.0
H2 C:ACT404 4.5 40.9 1.0
HG21 C:THR104 4.6 32.5 1.0
N C:GLU106 4.6 17.6 1.0
HG22 C:THR104 4.6 32.5 1.0
HG2 C:GLU106 4.6 30.7 1.0
CG2 C:THR104 4.7 27.1 1.0
H1 C:ACT404 4.8 40.9 1.0
HG1 C:THR104 4.8 24.2 1.0
CB C:GLU106 4.8 22.1 1.0
HA C:THR104 4.9 18.6 1.0
O C:HOH643 4.9 31.6 1.0
OG1 C:THR104 4.9 20.1 1.0
O C:HOH503 5.0 34.4 1.0
CB C:MET105 5.0 16.5 1.0

Zinc binding site 6 out of 6 in 4wnc

Go back to Zinc Binding Sites List in 4wnc
Zinc binding site 6 out of 6 in the Crystal Structure of Human Wild-Type Gapdh at 1.99 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Human Wild-Type Gapdh at 1.99 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:18.2
occ:0.91
 O E:HOH505 1.9 14.4 1.0
OXT E:GLU335 2.1 30.2 1.0
O E:HOH510 2.5 16.3 1.0
C E:GLU335 3.1 40.1 1.0
O E:GLU335 3.3 42.6 1.0
HG3 E:GLU335 4.1 20.8 1.0
O E:HOH515 4.2 31.0 1.0
HB2 E:GLU335 4.4 18.7 1.0
CA E:GLU335 4.5 25.4 1.0
CB E:GLU335 4.8 15.6 1.0
O E:ALA332 4.8 14.8 1.0
CG E:GLU335 4.9 17.3 1.0

Reference:

M.R.White, M.M.Khan, D.Deredge, C.R.Ross, R.Quintyn, B.E.Zucconi, V.H.Wysocki, P.L.Wintrode, G.M.Wilson, E.D.Garcin. A Dimer Interface Mutation in Glyceraldehyde 3-Phosphate Dehydrogenase Regulates Its Binding to Au-Rich Rna J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
Page generated: Sun Oct 27 09:59:12 2024

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