Atomistry » Zinc » PDB 4w6z-4wni » 4wnc
Atomistry »
  Zinc »
    PDB 4w6z-4wni »
      4wnc »

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

Go back to Zinc Binding Sites List in 4wnc
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

Go back to Zinc Binding Sites List in 4wnc
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy