Zinc in PDB 8vmz: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 40S
Protein crystallography data
The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 40S, PDB code: 8vmz
was solved by
C.Chang,
Y.Gao,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.84 /
1.57
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
113.88,
113.88,
88.22,
90,
90,
120
|
R / Rfree (%)
|
18.1 /
19.6
|
Other elements in 8vmz:
The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 40S also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 40S
(pdb code 8vmz). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 40S, PDB code: 8vmz:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8vmz
Go back to
Zinc Binding Sites List in 8vmz
Zinc binding site 1 out
of 4 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 40S
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 40S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn601
b:13.9
occ:1.00
|
ND1
|
A:HIS134
|
2.1
|
12.1
|
1.0
|
SG
|
A:CYS132
|
2.3
|
13.8
|
1.0
|
SG
|
A:CYS138
|
2.3
|
12.7
|
1.0
|
SG
|
A:CYS125
|
2.3
|
14.5
|
1.0
|
CE1
|
A:HIS134
|
2.9
|
14.0
|
1.0
|
CG
|
A:HIS134
|
3.2
|
12.4
|
1.0
|
CB
|
A:CYS138
|
3.3
|
13.4
|
1.0
|
CB
|
A:CYS125
|
3.3
|
12.2
|
1.0
|
CB
|
A:CYS132
|
3.3
|
12.6
|
1.0
|
CB
|
A:HIS134
|
3.7
|
12.1
|
1.0
|
O
|
A:HOH791
|
3.8
|
16.4
|
1.0
|
N
|
A:CYS138
|
4.0
|
12.4
|
1.0
|
CA
|
A:CYS132
|
4.0
|
13.5
|
1.0
|
NE2
|
A:HIS134
|
4.1
|
14.9
|
1.0
|
N
|
A:HIS134
|
4.2
|
14.7
|
1.0
|
CA
|
A:CYS138
|
4.2
|
9.7
|
1.0
|
CD2
|
A:HIS134
|
4.2
|
14.2
|
1.0
|
NH1
|
A:ARG122
|
4.3
|
12.7
|
1.0
|
N
|
A:VAL133
|
4.6
|
15.2
|
1.0
|
CA
|
A:HIS134
|
4.6
|
13.5
|
1.0
|
C
|
A:CYS132
|
4.6
|
15.8
|
1.0
|
CA
|
A:CYS125
|
4.7
|
12.1
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8vmz
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Zinc Binding Sites List in 8vmz
Zinc binding site 2 out
of 4 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 40S
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 40S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn602
b:12.6
occ:1.00
|
ND1
|
A:HIS110
|
2.1
|
13.9
|
1.0
|
SG
|
A:CYS105
|
2.3
|
11.8
|
1.0
|
SG
|
A:CYS100
|
2.3
|
12.3
|
1.0
|
SG
|
A:CYS41
|
2.3
|
14.6
|
1.0
|
CE1
|
A:HIS110
|
3.0
|
12.9
|
1.0
|
CB
|
A:CYS105
|
3.0
|
10.6
|
1.0
|
CB
|
A:CYS100
|
3.1
|
12.8
|
1.0
|
CG
|
A:HIS110
|
3.1
|
10.4
|
1.0
|
CB
|
A:CYS41
|
3.3
|
13.0
|
1.0
|
CB
|
A:HIS110
|
3.5
|
14.0
|
1.0
|
CA
|
A:CYS41
|
3.7
|
10.3
|
1.0
|
NE2
|
A:HIS110
|
4.2
|
12.6
|
1.0
|
CD2
|
A:HIS110
|
4.2
|
13.1
|
1.0
|
CB
|
A:ASN102
|
4.5
|
13.6
|
1.0
|
N
|
A:CYS41
|
4.5
|
11.6
|
1.0
|
ND2
|
A:ASN102
|
4.5
|
15.0
|
1.0
|
CA
|
A:CYS105
|
4.5
|
11.5
|
1.0
|
CA
|
A:CYS100
|
4.5
|
12.1
|
1.0
|
CB
|
A:ASN107
|
4.6
|
12.0
|
1.0
|
O
|
A:HIS40
|
4.8
|
13.2
|
1.0
|
C
|
A:CYS41
|
4.8
|
14.7
|
1.0
|
N
|
A:TYR42
|
4.9
|
11.8
|
1.0
|
C
|
A:HIS40
|
4.9
|
11.6
|
1.0
|
O
|
A:ASN102
|
5.0
|
14.1
|
1.0
|
CG
|
A:ASN102
|
5.0
|
15.4
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8vmz
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Zinc Binding Sites List in 8vmz
Zinc binding site 3 out
of 4 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 40S
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 40S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn401
b:13.5
occ:1.00
|
ND1
|
B:HIS334
|
2.1
|
14.0
|
1.0
|
SG
|
B:CYS332
|
2.3
|
13.0
|
1.0
|
SG
|
B:CYS338
|
2.3
|
13.0
|
1.0
|
SG
|
B:CYS325
|
2.3
|
13.1
|
1.0
|
CE1
|
B:HIS334
|
2.9
|
15.0
|
1.0
|
CG
|
B:HIS334
|
3.2
|
14.4
|
1.0
|
CB
|
B:CYS332
|
3.2
|
14.1
|
1.0
|
CB
|
B:CYS338
|
3.2
|
11.9
|
1.0
|
CB
|
B:CYS325
|
3.3
|
10.4
|
1.0
|
CB
|
B:HIS334
|
3.7
|
13.9
|
1.0
|
O
|
B:HOH602
|
3.8
|
17.4
|
1.0
|
CA
|
B:CYS332
|
4.0
|
12.4
|
1.0
|
N
|
B:CYS338
|
4.0
|
13.1
|
1.0
|
NE2
|
B:HIS334
|
4.1
|
14.8
|
1.0
|
N
|
B:HIS334
|
4.2
|
14.1
|
1.0
|
CA
|
B:CYS338
|
4.2
|
12.9
|
1.0
|
CD2
|
B:HIS334
|
4.2
|
14.0
|
1.0
|
NH1
|
B:ARG322
|
4.4
|
13.1
|
1.0
|
CA
|
B:HIS334
|
4.6
|
12.0
|
1.0
|
N
|
B:VAL333
|
4.6
|
13.8
|
1.0
|
C
|
B:CYS332
|
4.6
|
16.2
|
1.0
|
CA
|
B:CYS325
|
4.7
|
11.8
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8vmz
Go back to
Zinc Binding Sites List in 8vmz
Zinc binding site 4 out
of 4 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 40S
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 40S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:13.2
occ:1.00
|
ND1
|
B:HIS310
|
2.1
|
12.9
|
1.0
|
SG
|
B:CYS305
|
2.3
|
11.9
|
1.0
|
SG
|
B:CYS300
|
2.3
|
12.0
|
1.0
|
SG
|
B:CYS241
|
2.3
|
13.4
|
1.0
|
CE1
|
B:HIS310
|
3.0
|
14.1
|
1.0
|
CB
|
B:CYS305
|
3.0
|
13.7
|
1.0
|
CB
|
B:CYS300
|
3.1
|
12.6
|
1.0
|
CG
|
B:HIS310
|
3.1
|
12.0
|
1.0
|
CB
|
B:CYS241
|
3.2
|
11.9
|
1.0
|
CB
|
B:HIS310
|
3.5
|
12.0
|
1.0
|
CA
|
B:CYS241
|
3.7
|
12.5
|
1.0
|
NE2
|
B:HIS310
|
4.2
|
13.2
|
1.0
|
CD2
|
B:HIS310
|
4.2
|
12.6
|
1.0
|
CB
|
B:ASN302
|
4.5
|
11.7
|
1.0
|
CA
|
B:CYS305
|
4.5
|
11.4
|
1.0
|
N
|
B:CYS241
|
4.5
|
12.5
|
1.0
|
CA
|
B:CYS300
|
4.5
|
12.7
|
1.0
|
ND2
|
B:ASN302
|
4.6
|
13.6
|
1.0
|
CB
|
B:ASN307
|
4.6
|
12.2
|
1.0
|
C
|
B:CYS241
|
4.8
|
15.8
|
1.0
|
O
|
B:HIS240
|
4.9
|
14.0
|
1.0
|
N
|
B:TYR242
|
4.9
|
12.7
|
1.0
|
O
|
B:ASN302
|
5.0
|
14.2
|
1.0
|
C
|
B:HIS240
|
5.0
|
13.7
|
1.0
|
|
Reference:
C.Chang,
Y.Gao.
Homing Endonuclease I-Ppoi-Dna Complex:Reaction with 500 Um MG2+ For 160S To Be Published.
Page generated: Thu Oct 31 12:53:23 2024
|