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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:

Copper (Cu) 4 atoms
Chlorine (Cl) 8 atoms

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

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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

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Zinc binding site 2 out of 8 in the The X-Ray Crystallographic Structure of Beta Carbonic Anhydrase From the C3 Dicot Pisum Sativum


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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 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 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 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

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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

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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

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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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