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
|