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Zinc in PDB 2dph: Crystal Structure of Formaldehyde Dismutase

Enzymatic activity of Crystal Structure of Formaldehyde Dismutase

All present enzymatic activity of Crystal Structure of Formaldehyde Dismutase:
1.2.99.4;

Protein crystallography data

The structure of Crystal Structure of Formaldehyde Dismutase, PDB code: 2dph was solved by T.Hasegawa, A.Yamano, H.Yanase, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.92 / 2.27
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 90.229, 90.229, 226.689, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Formaldehyde Dismutase (pdb code 2dph). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Formaldehyde Dismutase, PDB code: 2dph:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2dph

Go back to Zinc Binding Sites List in 2dph
Zinc binding site 1 out of 4 in the Crystal Structure of Formaldehyde Dismutase


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 Formaldehyde Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:31.1
occ:1.00
SG A:CYS110 2.3 27.3 1.0
SG A:CYS102 2.3 29.7 1.0
SG A:CYS99 2.3 29.1 1.0
SG A:CYS96 2.4 28.2 1.0
CB A:CYS102 3.3 29.5 1.0
CB A:CYS110 3.4 27.7 1.0
N A:CYS96 3.4 27.2 1.0
CB A:CYS99 3.4 28.7 1.0
CB A:CYS96 3.5 27.5 1.0
N A:GLY97 3.8 27.0 1.0
N A:CYS99 3.8 28.3 1.0
CA A:CYS110 3.8 27.7 1.0
CA A:CYS96 3.9 27.2 1.0
N A:GLU111 4.1 28.6 1.0
CA A:CYS99 4.2 28.7 1.0
CB A:ASN112 4.3 29.6 1.0
C A:CYS96 4.3 27.2 1.0
N A:ARG98 4.3 27.5 1.0
N A:ASN112 4.3 29.6 1.0
N A:CYS102 4.4 29.6 1.0
C A:CYS110 4.4 28.0 1.0
CA A:CYS102 4.4 29.5 1.0
C A:ALA95 4.5 27.0 1.0
CA A:ALA95 4.7 26.8 1.0
CA A:GLY97 4.7 27.2 1.0
C A:CYS99 4.8 28.8 1.0
O A:CYS99 4.9 28.7 1.0
C A:ARG98 4.9 28.1 1.0
CA A:ASN112 5.0 29.8 1.0
C A:GLY97 5.0 27.4 1.0

Zinc binding site 2 out of 4 in 2dph

Go back to Zinc Binding Sites List in 2dph
Zinc binding site 2 out of 4 in the Crystal Structure of Formaldehyde Dismutase


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 Formaldehyde Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:37.5
occ:1.00
OD2 A:ASP169 1.9 24.4 1.0
NE2 A:HIS66 2.2 28.1 1.0
SG A:CYS45 2.3 29.3 1.0
C5N A:NAD1403 2.9 35.1 1.0
CD2 A:HIS66 3.1 27.1 1.0
CG A:ASP169 3.1 23.3 1.0
CE1 A:HIS66 3.2 28.6 1.0
CB A:CYS45 3.2 28.2 1.0
OD1 A:ASP169 3.6 25.6 1.0
C6N A:NAD1403 3.6 35.4 1.0
C4N A:NAD1403 3.8 34.9 1.0
OG A:SER47 3.8 27.8 1.0
CB A:SER47 4.0 26.5 1.0
CG A:HIS66 4.2 27.3 1.0
ND1 A:HIS66 4.3 28.4 1.0
CB A:ASP169 4.3 22.3 1.0
CG2 A:ILE170 4.3 21.2 1.0
OE2 A:GLU67 4.4 23.9 1.0
CD A:GLU67 4.5 24.5 1.0
CG A:GLU67 4.5 25.3 1.0
CA A:CYS45 4.7 27.8 1.0
CZ A:PHE126 4.8 37.2 1.0
N A:SER47 4.9 26.4 1.0
N1N A:NAD1403 4.9 34.4 1.0
O A:HOH1463 4.9 30.7 1.0

Zinc binding site 3 out of 4 in 2dph

Go back to Zinc Binding Sites List in 2dph
Zinc binding site 3 out of 4 in the Crystal Structure of Formaldehyde Dismutase


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 Formaldehyde Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1003

b:29.6
occ:1.00
SG B:CYS102 2.3 26.7 1.0
SG B:CYS99 2.3 27.2 1.0
SG B:CYS96 2.4 27.8 1.0
SG B:CYS110 2.4 27.0 1.0
N B:CYS96 3.3 27.2 1.0
CB B:CYS110 3.4 27.0 1.0
CB B:CYS102 3.4 26.3 1.0
CB B:CYS99 3.4 27.3 1.0
CB B:CYS96 3.4 27.4 1.0
CA B:CYS110 3.7 26.8 1.0
CA B:CYS96 3.8 27.3 1.0
N B:GLY97 3.8 26.8 1.0
N B:CYS99 3.9 27.1 1.0
N B:GLU111 4.0 27.6 1.0
CB B:ASN112 4.2 29.0 1.0
CA B:CYS99 4.2 27.2 1.0
C B:CYS96 4.3 27.2 1.0
C B:CYS110 4.3 27.1 1.0
N B:ASN112 4.3 28.8 1.0
N B:CYS102 4.4 26.1 1.0
C B:ALA95 4.4 27.2 1.0
N B:ARG98 4.4 26.8 1.0
CA B:CYS102 4.5 26.3 1.0
CA B:ALA95 4.6 27.2 1.0
CB B:ALA95 4.9 27.0 1.0
CA B:GLY97 4.9 26.6 1.0
C B:CYS99 4.9 27.3 1.0
CA B:ASN112 4.9 29.0 1.0
O B:CYS99 4.9 27.2 1.0

Zinc binding site 4 out of 4 in 2dph

Go back to Zinc Binding Sites List in 2dph
Zinc binding site 4 out of 4 in the Crystal Structure of Formaldehyde Dismutase


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 Formaldehyde Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1004

b:38.7
occ:1.00
OD2 B:ASP169 2.0 32.8 1.0
NE2 B:HIS66 2.1 34.7 1.0
SG B:CYS45 2.3 33.1 1.0
C5N B:NAD2403 2.8 41.9 1.0
CD2 B:HIS66 3.0 34.0 1.0
CE1 B:HIS66 3.1 34.8 1.0
CG B:ASP169 3.1 30.2 1.0
CB B:CYS45 3.2 32.4 1.0
C6N B:NAD2403 3.5 42.0 1.0
OD1 B:ASP169 3.6 31.6 1.0
OG B:SER47 3.7 33.4 1.0
C4N B:NAD2403 3.7 41.8 1.0
CB B:SER47 4.0 32.6 1.0
ND1 B:HIS66 4.2 33.9 1.0
CG B:HIS66 4.2 33.7 1.0
CG2 B:ILE170 4.3 27.3 1.0
CB B:ASP169 4.3 29.4 1.0
CG B:GLU67 4.5 30.9 1.0
OE2 B:GLU67 4.5 31.0 1.0
CD B:GLU67 4.5 30.4 1.0
CA B:CYS45 4.7 32.2 1.0
N1N B:NAD2403 4.8 41.5 1.0
N B:SER47 4.8 32.0 1.0
C3N B:NAD2403 4.9 42.3 1.0
O B:HOH2412 5.0 22.1 1.0

Reference:

T.Hasegawa, A.Yamano, K.Miura, Y.Katsube, H.Yanase, N.Kato. The X-Ray Crystal Structure of Formaldehyde Dismutase at 2.3 A Resolution Acta Crystallogr.,Sect.A V. 58 C102 2002.
ISSN: ISSN 0108-7673
Page generated: Wed Oct 16 22:49:13 2024

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