Atomistry » Zinc » PDB 6iiv-6iu5 » 6im1
Atomistry »
  Zinc »
    PDB 6iiv-6iu5 »
      6im1 »

Zinc in PDB 6im1: Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1

Enzymatic activity of Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1

All present enzymatic activity of Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1:
4.2.1.1;

Protein crystallography data

The structure of Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1, PDB code: 6im1 was solved by M.S.Jin, S.Kim, J.Sung, J.Yeon, S.H.Choi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 124.07 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 118.924, 120.068, 124.067, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.6

Other elements in 6im1:

The structure of Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1 also contains other interesting chemical elements:

Calcium (Ca) 15 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1 (pdb code 6im1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1, PDB code: 6im1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6im1

Go back to Zinc Binding Sites List in 6im1
Zinc binding site 1 out of 6 in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1


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 A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:32.4
occ:1.00
 O A:HOH406 2.0 37.6 1.0
NE2 A:HIS107 2.1 29.8 1.0
ND1 A:HIS126 2.2 25.4 1.0
NE2 A:HIS109 2.2 27.2 1.0
CD2 A:HIS107 2.9 25.7 1.0
CE1 A:HIS126 3.0 25.4 1.0
CD2 A:HIS109 3.1 27.0 1.0
CE1 A:HIS107 3.1 29.0 1.0
CE1 A:HIS109 3.2 26.2 1.0
CG A:HIS126 3.2 22.5 1.0
CB A:HIS126 3.6 21.9 1.0
O A:HOH513 3.7 37.3 1.0
OG1 A:THR193 3.8 25.4 1.0
OE1 A:GLU113 3.8 32.5 1.0
O A:HOH514 4.0 40.4 1.0
CG A:HIS107 4.1 23.0 1.0
ND1 A:HIS107 4.2 25.9 1.0
NE2 A:HIS126 4.2 23.4 1.0
CG A:HIS109 4.2 24.3 1.0
ND1 A:HIS109 4.3 26.6 1.0
CD2 A:HIS126 4.3 23.2 1.0
CD A:GLU113 4.9 30.3 1.0

Zinc binding site 2 out of 6 in 6im1

Go back to Zinc Binding Sites List in 6im1
Zinc binding site 2 out of 6 in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1


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 A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:34.4
occ:1.00
 O B:HOH402 2.1 36.2 1.0
NE2 B:HIS107 2.1 28.4 1.0
ND1 B:HIS126 2.2 24.1 1.0
NE2 B:HIS109 2.2 28.4 1.0
CD2 B:HIS107 3.0 31.7 1.0
CE1 B:HIS126 3.0 26.5 1.0
CD2 B:HIS109 3.1 25.9 1.0
CE1 B:HIS107 3.2 31.4 1.0
CE1 B:HIS109 3.2 29.0 1.0
CG B:HIS126 3.2 26.5 1.0
CB B:HIS126 3.7 23.8 1.0
O B:HOH494 3.7 42.8 1.0
OG1 B:THR193 3.8 26.2 1.0
OE1 B:GLU113 3.8 30.4 1.0
O B:HOH500 4.0 39.8 1.0
CG B:HIS107 4.2 26.3 1.0
NE2 B:HIS126 4.2 25.8 1.0
ND1 B:HIS107 4.2 23.8 1.0
CG B:HIS109 4.2 25.5 1.0
ND1 B:HIS109 4.3 28.6 1.0
CD2 B:HIS126 4.3 25.6 1.0
CD B:GLU113 4.8 29.9 1.0

Zinc binding site 3 out of 6 in 6im1

Go back to Zinc Binding Sites List in 6im1
Zinc binding site 3 out of 6 in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1


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 A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:51.7
occ:1.00
 NE2 C:HIS107 2.1 46.2 1.0
NE2 C:HIS109 2.1 48.4 1.0
O C:HOH440 2.2 75.6 1.0
ND1 C:HIS126 2.2 45.1 1.0
CD2 C:HIS107 3.0 44.5 1.0
CD2 C:HIS109 3.1 41.8 1.0
CE1 C:HIS126 3.1 45.2 1.0
CE1 C:HIS109 3.1 44.1 1.0
CE1 C:HIS107 3.1 45.5 1.0
CG C:HIS126 3.2 42.3 1.0
CB C:HIS126 3.6 44.0 1.0
OG1 C:THR193 3.8 41.3 1.0
OE1 C:GLU113 3.8 55.4 1.0
CG C:HIS107 4.2 47.2 1.0
ND1 C:HIS107 4.2 49.8 1.0
ND1 C:HIS109 4.2 43.9 1.0
CG C:HIS109 4.2 47.8 1.0
NE2 C:HIS126 4.2 41.7 1.0
CD2 C:HIS126 4.3 44.4 1.0
O C:HOH448 4.4 58.1 1.0
CD C:GLU113 4.9 55.2 1.0

Zinc binding site 4 out of 6 in 6im1

Go back to Zinc Binding Sites List in 6im1
Zinc binding site 4 out of 6 in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1


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 A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:48.4
occ:1.00
 O D:HOH407 2.0 52.6 1.0
NE2 D:HIS107 2.1 44.2 1.0
ND1 D:HIS126 2.2 36.7 1.0
NE2 D:HIS109 2.2 46.4 1.0
CD2 D:HIS107 3.0 46.4 1.0
CE1 D:HIS126 3.0 38.0 1.0
CE1 D:HIS107 3.1 48.4 1.0
CD2 D:HIS109 3.1 42.6 1.0
CE1 D:HIS109 3.2 43.8 1.0
CG D:HIS126 3.2 34.5 1.0
CB D:HIS126 3.6 37.4 1.0
OG1 D:THR193 3.8 40.4 1.0
OE1 D:GLU113 3.8 46.0 1.0
CG D:HIS107 4.1 43.1 1.0
ND1 D:HIS107 4.1 43.0 1.0
NE2 D:HIS126 4.2 38.0 1.0
O D:HOH440 4.2 49.4 1.0
ND1 D:HIS109 4.3 39.0 1.0
CD2 D:HIS126 4.3 36.0 1.0
CG D:HIS109 4.3 44.6 1.0
CD D:GLU113 4.9 43.6 1.0

Zinc binding site 5 out of 6 in 6im1

Go back to Zinc Binding Sites List in 6im1
Zinc binding site 5 out of 6 in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:44.6
occ:1.00
 NE2 E:HIS107 2.1 35.3 1.0
O E:HOH406 2.1 47.8 1.0
NE2 E:HIS109 2.1 37.0 1.0
ND1 E:HIS126 2.1 33.1 1.0
CD2 E:HIS107 2.9 37.1 1.0
CE1 E:HIS126 3.0 30.1 1.0
CD2 E:HIS109 3.0 37.6 1.0
CE1 E:HIS107 3.1 36.5 1.0
CE1 E:HIS109 3.1 40.3 1.0
CG E:HIS126 3.2 35.1 1.0
CB E:HIS126 3.6 34.9 1.0
OE1 E:GLU113 3.8 37.3 1.0
OG1 E:THR193 3.9 36.1 1.0
O E:HOH457 4.1 48.2 1.0
CG E:HIS107 4.1 34.3 1.0
ND1 E:HIS107 4.1 34.8 1.0
NE2 E:HIS126 4.1 31.4 1.0
ND1 E:HIS109 4.2 34.6 1.0
CG E:HIS109 4.2 35.4 1.0
CD2 E:HIS126 4.3 36.5 1.0
CD E:GLU113 4.9 39.9 1.0

Zinc binding site 6 out of 6 in 6im1

Go back to Zinc Binding Sites List in 6im1
Zinc binding site 6 out of 6 in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:46.2
occ:1.00
 NE2 F:HIS107 2.1 39.7 1.0
NE2 F:HIS109 2.1 38.1 1.0
O F:HOH402 2.2 54.8 1.0
ND1 F:HIS126 2.2 33.4 1.0
CD2 F:HIS107 3.0 39.8 1.0
CD2 F:HIS109 3.0 40.0 1.0
CE1 F:HIS126 3.0 35.8 1.0
CE1 F:HIS109 3.1 44.4 1.0
CE1 F:HIS107 3.1 36.5 1.0
CG F:HIS126 3.3 30.8 1.0
CB F:HIS126 3.7 34.6 1.0
OE1 F:GLU113 3.8 42.5 1.0
OG1 F:THR193 3.8 38.3 1.0
O F:HOH462 3.9 56.1 1.0
CG F:HIS107 4.1 36.5 1.0
ND1 F:HIS107 4.2 42.0 1.0
CG F:HIS109 4.2 38.7 1.0
ND1 F:HIS109 4.2 38.9 1.0
NE2 F:HIS126 4.2 33.9 1.0
CD2 F:HIS126 4.3 33.3 1.0
CD F:GLU113 4.9 41.4 1.0

Reference:

S.Kim, J.Sung, J.Yeon, S.H.Choi, M.S.Jin. Crystal Structure of A Highly Thermostable Alpha-Carbonic Anhydrase From Persephonella Marina Ex-H1. Mol.Cells V. 42 460 2019.
ISSN: ISSN 1016-8478
PubMed: 31250619
DOI: 10.14348/MOLCELLS.2019.0029
Page generated: Mon Oct 28 23:52:59 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy