Zinc in PDB 1ekj: The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum
Enzymatic activity of The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum
All present enzymatic activity of The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum:
4.2.1.1;
Protein crystallography data
The structure of The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum, PDB code: 1ekj
was solved by
M.S.Kimber,
E.F.Pai,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.00 /
1.93
|
Space group
|
C 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
136.909,
143.318,
202.135,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.9 /
25
|
Other elements in 1ekj:
The structure of The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum
(pdb code 1ekj). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum, PDB code: 1ekj:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 1ekj
Go back to
Zinc Binding Sites List in 1ekj
Zinc binding site 1 out
of 8 in the The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn4001
b:46.1
occ:1.00
|
NE2
|
A:HIS220
|
2.1
|
51.8
|
1.0
|
SG
|
A:CYS223
|
2.3
|
40.6
|
1.0
|
SG
|
A:CYS160
|
2.3
|
50.5
|
1.0
|
OXT
|
A:ACT3001
|
2.7
|
68.8
|
1.0
|
CE1
|
A:HIS220
|
3.0
|
51.5
|
1.0
|
CD2
|
A:HIS220
|
3.1
|
50.5
|
1.0
|
CB
|
A:CYS160
|
3.1
|
50.3
|
1.0
|
C
|
A:ACT3001
|
3.3
|
69.8
|
1.0
|
CB
|
A:CYS223
|
3.4
|
46.3
|
1.0
|
CA
|
A:CYS223
|
3.7
|
48.1
|
1.0
|
CH3
|
A:ACT3001
|
3.9
|
68.7
|
1.0
|
CB
|
A:ASP162
|
4.0
|
52.3
|
1.0
|
O
|
A:ACT3001
|
4.0
|
68.9
|
1.0
|
ND1
|
A:HIS220
|
4.1
|
52.7
|
1.0
|
N
|
A:GLY224
|
4.1
|
48.2
|
1.0
|
CG
|
A:HIS220
|
4.1
|
51.5
|
1.0
|
CA
|
A:ALA185
|
4.2
|
38.3
|
1.0
|
OD2
|
A:ASP162
|
4.3
|
51.9
|
1.0
|
N
|
A:ALA185
|
4.3
|
39.1
|
1.0
|
C
|
A:CYS223
|
4.3
|
48.5
|
1.0
|
O
|
A:HOH1120
|
4.4
|
38.7
|
1.0
|
CA
|
A:CYS160
|
4.6
|
51.4
|
1.0
|
N
|
A:GLY225
|
4.6
|
48.7
|
1.0
|
CG
|
A:ASP162
|
4.7
|
52.0
|
1.0
|
ND2
|
A:ASN186
|
4.7
|
35.6
|
1.0
|
N
|
A:ASP162
|
4.9
|
51.8
|
1.0
|
N
|
A:CYS223
|
4.9
|
48.6
|
1.0
|
|
Zinc binding site 2 out
of 8 in 1ekj
Go back to
Zinc Binding Sites List in 1ekj
Zinc binding site 2 out
of 8 in the The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn4002
b:62.6
occ:1.00
|
NE2
|
B:HIS220
|
2.0
|
60.6
|
1.0
|
OXT
|
A:ACT3003
|
2.3
|
80.3
|
1.0
|
SG
|
B:CYS160
|
2.3
|
55.1
|
1.0
|
SG
|
B:CYS223
|
2.3
|
61.5
|
1.0
|
CE1
|
B:HIS220
|
2.9
|
61.0
|
1.0
|
CD2
|
B:HIS220
|
3.1
|
60.9
|
1.0
|
C
|
A:ACT3003
|
3.2
|
80.3
|
1.0
|
CB
|
B:CYS223
|
3.2
|
62.7
|
1.0
|
CA
|
B:CYS223
|
3.4
|
62.7
|
1.0
|
CB
|
B:CYS160
|
3.5
|
56.6
|
1.0
|
O
|
A:ACT3003
|
3.8
|
79.8
|
1.0
|
CB
|
B:ASP162
|
4.0
|
64.8
|
1.0
|
ND1
|
B:HIS220
|
4.0
|
61.1
|
1.0
|
N
|
B:GLY224
|
4.0
|
62.4
|
1.0
|
C
|
B:CYS223
|
4.1
|
62.2
|
1.0
|
CG
|
B:HIS220
|
4.1
|
60.6
|
1.0
|
CH3
|
A:ACT3003
|
4.1
|
79.6
|
1.0
|
OD2
|
B:ASP162
|
4.3
|
64.6
|
1.0
|
CA
|
B:ALA185
|
4.4
|
55.9
|
1.0
|
N
|
B:ALA185
|
4.5
|
55.3
|
1.0
|
CG
|
B:ASP162
|
4.5
|
65.7
|
1.0
|
N
|
B:GLY225
|
4.5
|
64.8
|
1.0
|
N
|
B:CYS223
|
4.7
|
65.2
|
1.0
|
O
|
B:ALA222
|
4.7
|
67.0
|
1.0
|
CA
|
B:CYS160
|
4.8
|
56.1
|
1.0
|
|
Zinc binding site 3 out
of 8 in 1ekj
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Zinc Binding Sites List in 1ekj
Zinc binding site 3 out
of 8 in the The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn4003
b:31.2
occ:1.00
|
O
|
C:HOH1001
|
2.0
|
26.1
|
1.0
|
NE2
|
C:HIS220
|
2.1
|
28.4
|
1.0
|
SG
|
C:CYS160
|
2.3
|
26.6
|
1.0
|
SG
|
C:CYS223
|
2.3
|
30.3
|
1.0
|
CE1
|
C:HIS220
|
3.0
|
30.2
|
1.0
|
CD2
|
C:HIS220
|
3.1
|
28.7
|
1.0
|
CB
|
C:CYS160
|
3.2
|
24.8
|
1.0
|
CB
|
C:CYS223
|
3.2
|
33.4
|
1.0
|
CA
|
C:CYS223
|
3.5
|
34.3
|
1.0
|
OXT
|
C:ACT3007
|
3.5
|
37.0
|
1.0
|
C
|
C:ACT3007
|
3.7
|
34.5
|
1.0
|
CB
|
C:ASP162
|
3.9
|
24.8
|
1.0
|
CH3
|
C:ACT3007
|
4.0
|
30.4
|
1.0
|
N
|
C:GLY224
|
4.1
|
31.6
|
1.0
|
OD2
|
C:ASP162
|
4.1
|
26.2
|
1.0
|
C
|
C:CYS223
|
4.2
|
34.1
|
1.0
|
ND1
|
C:HIS220
|
4.2
|
29.6
|
1.0
|
O
|
C:HOH1103
|
4.2
|
33.4
|
1.0
|
O
|
C:ACT3007
|
4.2
|
33.6
|
1.0
|
CG
|
C:HIS220
|
4.2
|
32.1
|
1.0
|
CA
|
C:ALA185
|
4.4
|
27.6
|
1.0
|
N
|
C:ALA185
|
4.5
|
28.2
|
1.0
|
CG
|
C:ASP162
|
4.5
|
27.0
|
1.0
|
CA
|
C:CYS160
|
4.7
|
27.8
|
1.0
|
N
|
C:GLY225
|
4.7
|
30.8
|
1.0
|
ND2
|
C:ASN186
|
4.7
|
27.9
|
1.0
|
N
|
C:CYS223
|
4.7
|
34.5
|
1.0
|
N
|
C:ASP162
|
4.9
|
23.9
|
1.0
|
CA
|
C:ASP162
|
5.0
|
26.1
|
1.0
|
|
Zinc binding site 4 out
of 8 in 1ekj
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Zinc Binding Sites List in 1ekj
Zinc binding site 4 out
of 8 in the The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn4004
b:25.8
occ:1.00
|
NE2
|
D:HIS220
|
2.0
|
22.3
|
1.0
|
SG
|
D:CYS160
|
2.2
|
21.9
|
1.0
|
SG
|
D:CYS223
|
2.4
|
22.1
|
1.0
|
CE1
|
D:HIS220
|
3.0
|
22.8
|
1.0
|
CD2
|
D:HIS220
|
3.1
|
21.9
|
1.0
|
CB
|
D:CYS160
|
3.1
|
19.2
|
1.0
|
CB
|
D:CYS223
|
3.2
|
21.7
|
1.0
|
OXT
|
C:ACT3004
|
3.5
|
38.2
|
1.0
|
CA
|
D:CYS223
|
3.5
|
24.1
|
1.0
|
C
|
C:ACT3004
|
3.8
|
33.5
|
1.0
|
CB
|
D:ASP162
|
3.9
|
27.4
|
1.0
|
CH3
|
C:ACT3004
|
4.0
|
28.8
|
1.0
|
N
|
D:GLY224
|
4.1
|
24.3
|
1.0
|
OD2
|
D:ASP162
|
4.1
|
30.2
|
1.0
|
ND1
|
D:HIS220
|
4.1
|
26.1
|
1.0
|
CG
|
D:HIS220
|
4.2
|
22.5
|
1.0
|
C
|
D:CYS223
|
4.2
|
23.4
|
1.0
|
O
|
D:HOH1022
|
4.3
|
19.2
|
1.0
|
CA
|
D:ALA185
|
4.4
|
21.9
|
1.0
|
O
|
C:ACT3004
|
4.4
|
29.6
|
1.0
|
N
|
D:ALA185
|
4.5
|
21.1
|
1.0
|
CG
|
D:ASP162
|
4.5
|
29.0
|
1.0
|
CA
|
D:CYS160
|
4.6
|
21.2
|
1.0
|
ND2
|
D:ASN186
|
4.7
|
17.7
|
1.0
|
N
|
D:CYS223
|
4.8
|
27.4
|
1.0
|
N
|
D:GLY225
|
4.8
|
27.3
|
1.0
|
N
|
D:ASP162
|
4.9
|
22.9
|
1.0
|
CA
|
D:ASP162
|
5.0
|
26.9
|
1.0
|
|
Zinc binding site 5 out
of 8 in 1ekj
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Zinc Binding Sites List in 1ekj
Zinc binding site 5 out
of 8 in the The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn4005
b:43.8
occ:1.00
|
NE2
|
E:HIS220
|
2.1
|
48.0
|
1.0
|
SG
|
E:CYS160
|
2.3
|
33.1
|
1.0
|
SG
|
E:CYS223
|
2.3
|
46.9
|
1.0
|
OXT
|
E:ACT3005
|
2.5
|
52.6
|
1.0
|
CE1
|
E:HIS220
|
2.9
|
47.7
|
1.0
|
CD2
|
E:HIS220
|
3.1
|
48.3
|
1.0
|
C
|
E:ACT3005
|
3.2
|
52.4
|
1.0
|
CB
|
E:CYS223
|
3.2
|
44.3
|
1.0
|
CB
|
E:CYS160
|
3.3
|
37.8
|
1.0
|
CA
|
E:CYS223
|
3.5
|
43.4
|
1.0
|
CH3
|
E:ACT3005
|
3.6
|
51.4
|
1.0
|
CB
|
E:ASP162
|
4.0
|
40.5
|
1.0
|
N
|
E:GLY224
|
4.0
|
41.8
|
1.0
|
ND1
|
E:HIS220
|
4.1
|
48.3
|
1.0
|
C
|
E:CYS223
|
4.1
|
42.5
|
1.0
|
OD2
|
E:ASP162
|
4.1
|
40.9
|
1.0
|
CG
|
E:HIS220
|
4.2
|
49.2
|
1.0
|
O
|
E:ACT3005
|
4.2
|
51.1
|
1.0
|
O
|
E:HOH1083
|
4.3
|
33.2
|
1.0
|
CA
|
E:ALA185
|
4.4
|
36.3
|
1.0
|
N
|
E:ALA185
|
4.5
|
35.1
|
1.0
|
CG
|
E:ASP162
|
4.6
|
41.3
|
1.0
|
CA
|
E:CYS160
|
4.7
|
37.6
|
1.0
|
N
|
E:CYS223
|
4.7
|
44.7
|
1.0
|
N
|
E:GLY225
|
4.7
|
40.7
|
1.0
|
OD1
|
E:ASN186
|
4.8
|
35.0
|
1.0
|
N
|
E:ASP162
|
4.9
|
40.2
|
1.0
|
|
Zinc binding site 6 out
of 8 in 1ekj
Go back to
Zinc Binding Sites List in 1ekj
Zinc binding site 6 out
of 8 in the The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn4006
b:44.5
occ:1.00
|
NE2
|
F:HIS220
|
2.0
|
48.1
|
1.0
|
SG
|
F:CYS223
|
2.3
|
40.3
|
1.0
|
SG
|
F:CYS160
|
2.3
|
40.4
|
1.0
|
CE1
|
F:HIS220
|
2.9
|
48.0
|
1.0
|
OXT
|
F:ACT3008
|
3.1
|
59.9
|
1.0
|
CD2
|
F:HIS220
|
3.1
|
48.1
|
1.0
|
CB
|
F:CYS160
|
3.3
|
42.0
|
1.0
|
C
|
F:ACT3008
|
3.3
|
59.3
|
1.0
|
CB
|
F:CYS223
|
3.4
|
43.6
|
1.0
|
CA
|
F:CYS223
|
3.6
|
44.4
|
1.0
|
CH3
|
F:ACT3008
|
3.8
|
58.1
|
1.0
|
O
|
F:ACT3008
|
3.9
|
59.5
|
1.0
|
CB
|
F:ASP162
|
4.0
|
41.6
|
1.0
|
ND1
|
F:HIS220
|
4.1
|
47.6
|
1.0
|
N
|
F:GLY224
|
4.1
|
45.1
|
1.0
|
CG
|
F:HIS220
|
4.1
|
48.6
|
1.0
|
OD2
|
F:ASP162
|
4.2
|
41.9
|
1.0
|
CA
|
F:ALA185
|
4.3
|
38.5
|
1.0
|
C
|
F:CYS223
|
4.3
|
44.9
|
1.0
|
N
|
F:ALA185
|
4.4
|
38.4
|
1.0
|
O
|
F:HOH1335
|
4.5
|
40.1
|
1.0
|
N
|
F:GLY225
|
4.6
|
43.7
|
1.0
|
CG
|
F:ASP162
|
4.6
|
42.2
|
1.0
|
CA
|
F:CYS160
|
4.7
|
41.8
|
1.0
|
N
|
F:CYS223
|
4.9
|
46.0
|
1.0
|
OD1
|
F:ASN186
|
4.9
|
36.9
|
1.0
|
N
|
F:ASP162
|
4.9
|
41.4
|
1.0
|
|
Zinc binding site 7 out
of 8 in 1ekj
Go back to
Zinc Binding Sites List in 1ekj
Zinc binding site 7 out
of 8 in the The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn4007
b:28.8
occ:1.00
|
NE2
|
G:HIS220
|
2.0
|
29.9
|
1.0
|
SG
|
G:CYS223
|
2.2
|
28.6
|
1.0
|
SG
|
G:CYS160
|
2.4
|
26.9
|
1.0
|
OXT
|
G:ACT3002
|
2.6
|
43.9
|
1.0
|
CE1
|
G:HIS220
|
3.0
|
28.8
|
1.0
|
CD2
|
G:HIS220
|
3.1
|
31.0
|
1.0
|
CB
|
G:CYS223
|
3.2
|
30.1
|
1.0
|
CB
|
G:CYS160
|
3.2
|
23.9
|
1.0
|
C
|
G:ACT3002
|
3.3
|
41.9
|
1.0
|
CA
|
G:CYS223
|
3.5
|
30.6
|
1.0
|
CH3
|
G:ACT3002
|
3.7
|
41.9
|
1.0
|
CB
|
G:ASP162
|
3.8
|
22.5
|
1.0
|
OD2
|
G:ASP162
|
4.1
|
26.9
|
1.0
|
ND1
|
G:HIS220
|
4.1
|
31.3
|
1.0
|
CG
|
G:HIS220
|
4.2
|
31.1
|
1.0
|
N
|
G:GLY224
|
4.2
|
28.6
|
1.0
|
C
|
G:CYS223
|
4.2
|
29.4
|
1.0
|
O
|
G:ACT3002
|
4.2
|
36.5
|
1.0
|
O
|
G:HOH1035
|
4.3
|
26.9
|
1.0
|
CA
|
G:ALA185
|
4.3
|
21.5
|
1.0
|
N
|
G:ALA185
|
4.4
|
21.3
|
1.0
|
CG
|
G:ASP162
|
4.5
|
25.2
|
1.0
|
CA
|
G:CYS160
|
4.6
|
23.7
|
1.0
|
N
|
G:GLY225
|
4.7
|
31.8
|
1.0
|
OD1
|
G:ASN186
|
4.8
|
25.2
|
1.0
|
N
|
G:CYS223
|
4.8
|
32.3
|
1.0
|
N
|
G:ASP162
|
4.9
|
24.9
|
1.0
|
CA
|
G:ASP162
|
5.0
|
26.3
|
1.0
|
|
Zinc binding site 8 out
of 8 in 1ekj
Go back to
Zinc Binding Sites List in 1ekj
Zinc binding site 8 out
of 8 in the The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn4008
b:24.4
occ:1.00
|
NE2
|
H:HIS220
|
2.0
|
23.9
|
1.0
|
SG
|
H:CYS160
|
2.3
|
20.3
|
1.0
|
SG
|
H:CYS223
|
2.3
|
20.0
|
1.0
|
OXT
|
H:ACT3006
|
2.4
|
32.8
|
1.0
|
CE1
|
H:HIS220
|
2.9
|
21.9
|
1.0
|
CB
|
H:CYS160
|
3.0
|
18.5
|
1.0
|
CD2
|
H:HIS220
|
3.2
|
22.1
|
1.0
|
CB
|
H:CYS223
|
3.3
|
20.1
|
1.0
|
C
|
H:ACT3006
|
3.3
|
34.2
|
1.0
|
CA
|
H:CYS223
|
3.6
|
21.6
|
1.0
|
CH3
|
H:ACT3006
|
3.7
|
31.9
|
1.0
|
CB
|
H:ASP162
|
3.9
|
24.7
|
1.0
|
ND1
|
H:HIS220
|
4.1
|
23.7
|
1.0
|
OD2
|
H:ASP162
|
4.2
|
21.1
|
1.0
|
CG
|
H:HIS220
|
4.2
|
23.2
|
1.0
|
N
|
H:GLY224
|
4.2
|
26.4
|
1.0
|
C
|
H:CYS223
|
4.3
|
22.8
|
1.0
|
O
|
H:ACT3006
|
4.3
|
31.8
|
1.0
|
O
|
H:HOH1032
|
4.4
|
24.2
|
1.0
|
CA
|
H:ALA185
|
4.4
|
18.9
|
1.0
|
N
|
H:ALA185
|
4.5
|
18.6
|
1.0
|
CA
|
H:CYS160
|
4.5
|
17.2
|
1.0
|
CG
|
H:ASP162
|
4.6
|
24.8
|
1.0
|
ND2
|
H:ASN186
|
4.6
|
17.8
|
1.0
|
N
|
H:GLY225
|
4.8
|
26.3
|
1.0
|
N
|
H:CYS223
|
4.8
|
24.7
|
1.0
|
N
|
H:ASP162
|
4.9
|
21.3
|
1.0
|
CA
|
H:ASP162
|
5.0
|
23.2
|
1.0
|
|
Reference:
M.S.Kimber,
E.F.Pai.
The Active Site Architecture of Pisum Sativum Beta-Carbonic Anhydrase Is A Mirror Image of That of Alpha-Carbonic Anhydrases. Embo J. V. 19 1407 2000.
ISSN: ISSN 0261-4189
PubMed: 10747009
DOI: 10.1093/EMBOJ/19.7.1407
Page generated: Sun Oct 13 00:14:43 2024
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