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Sodium in PDB 9qez: Carbonic Anhydrase Mutant

Protein crystallography data

The structure of Carbonic Anhydrase Mutant, PDB code: 9qez was solved by I.Mohsin, A.C.Papageorgiou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.78 / 2.10
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.687, 164.962, 165.114, 90, 90, 90
R / Rfree (%) 20 / 24

Other elements in 9qez:

The structure of Carbonic Anhydrase Mutant also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Zinc (Zn) 12 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Sodium atom in the Carbonic Anhydrase Mutant (pdb code 9qez). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 13 binding sites of Sodium where determined in the Carbonic Anhydrase Mutant, PDB code: 9qez:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 13 in 9qez

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Sodium binding site 1 out of 13 in the Carbonic Anhydrase Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Carbonic Anhydrase Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na202

b:55.2
occ:1.00
 O D:ARG43 2.9 38.8 1.0
O D:ASN47 3.0 44.5 1.0
N D:ASN47 3.0 43.7 1.0
N D:GLU46 3.4 48.2 1.0
N D:ALA65 3.4 42.8 1.0
N D:ASP45 3.5 41.9 1.0
CD2 D:HIS64 3.6 39.4 1.0
C D:ASN47 3.7 46.3 1.0
CA D:GLY44 3.7 36.8 1.0
CB D:ALA65 3.8 45.4 1.0
CA D:ASN47 3.8 42.9 1.0
CB D:GLU46 3.9 49.9 1.0
C D:GLY44 3.9 43.3 1.0
CA D:GLU46 3.9 51.0 1.0
C D:GLU46 3.9 52.2 1.0
C D:ARG43 3.9 37.5 1.0
OD1 D:ASP45 4.0 41.0 1.0
NE2 D:HIS64 4.0 40.2 1.0
CA D:ALA65 4.1 46.6 1.0
C D:HIS64 4.1 40.5 1.0
C D:ASP45 4.2 49.7 1.0
O D:ALA65 4.2 46.8 1.0
CB D:ASN47 4.2 46.3 1.0
CA D:HIS64 4.3 40.7 1.0
CG D:HIS64 4.3 40.6 1.0
N D:GLY44 4.3 34.4 1.0
CA D:ASP45 4.4 44.9 1.0
C D:ALA65 4.5 49.3 1.0
CG D:GLU46 4.7 51.9 1.0
O D:GLY44 4.8 40.1 1.0
CG1 D:ILE49 4.8 34.5 1.0
CE1 D:HIS64 4.9 42.5 1.0
N D:SER48 4.9 42.5 1.0
CD1 D:ILE49 4.9 37.0 1.0
CB D:HIS64 4.9 38.4 1.0
O D:HIS64 5.0 40.7 1.0
CG D:ASP45 5.0 45.4 1.0

Sodium binding site 2 out of 13 in 9qez

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Sodium binding site 2 out of 13 in the Carbonic Anhydrase Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Carbonic Anhydrase Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na203

b:62.3
occ:1.00
 O F:HOH350 2.1 49.2 1.0
O A:HOH321 2.2 54.0 1.0
O D:GLY107 2.9 36.9 1.0
C D:GLY107 3.9 33.3 1.0
CA D:GLY107 4.1 33.2 1.0
CD1 A:ILE109 4.1 35.0 1.0
O A:GLY107 4.5 38.9 1.0
CA D:GLY125 4.6 38.0 1.0
CG1 A:ILE109 4.8 34.4 1.0

Sodium binding site 3 out of 13 in 9qez

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Sodium binding site 3 out of 13 in the Carbonic Anhydrase Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Carbonic Anhydrase Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na204

b:58.7
occ:1.00
 ND2 D:ASN56 2.3 46.3 0.3
ND2 D:ASN56 2.4 48.3 0.7
CB D:ALA163 2.5 59.0 1.0
O D:VAL85 3.0 37.1 1.0
O D:GLY54 3.0 39.5 1.0
CA D:ALA163 3.1 69.6 1.0
N D:ASN56 3.2 36.7 1.0
CG D:ASN56 3.3 43.6 0.3
CG D:ASN56 3.3 49.0 0.7
CB D:ASN56 3.5 42.2 0.7
OG1 D:THR86 3.5 45.7 1.0
CB D:ASN56 3.5 42.5 0.3
O D:ALA163 3.7 73.3 1.0
C D:VAL85 3.8 40.0 1.0
C D:THR55 3.8 39.7 1.0
C D:ALA163 3.9 74.2 1.0
CA D:THR55 3.9 38.1 1.0
CA D:ASN56 4.0 40.1 0.7
CA D:ASN56 4.0 40.1 0.3
C D:GLY54 4.1 42.0 1.0
CB D:ASN166 4.2 69.7 1.0
C D:TYR84 4.2 39.0 1.0
N D:ALA163 4.3 71.9 1.0
N D:THR86 4.4 36.2 1.0
CA D:THR86 4.4 40.4 1.0
N D:VAL85 4.4 35.9 1.0
O D:TYR84 4.4 39.4 1.0
OD1 D:ASN56 4.4 40.7 0.3
N D:THR55 4.4 34.7 1.0
CA D:TYR84 4.5 38.1 1.0
OD1 D:ASN56 4.5 45.6 0.7
CB D:THR86 4.5 40.5 1.0
CA D:VAL85 4.7 36.6 1.0
CG D:ASN166 4.8 69.4 1.0
O D:THR55 4.8 36.0 1.0

Sodium binding site 4 out of 13 in 9qez

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Sodium binding site 4 out of 13 in the Carbonic Anhydrase Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Carbonic Anhydrase Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na205

b:61.7
occ:1.00
 NZ D:LYS171 2.4 68.2 1.0
CE D:LYS171 2.8 76.2 1.0
O D:THR15 3.1 43.3 1.0
OD1 D:ASN35 3.1 60.8 1.0
OG D:SER170 3.5 68.6 1.0
CB D:PHE17 3.7 44.6 1.0
O D:SER34 3.7 37.9 1.0
O D:ASP33 3.7 40.8 1.0
N D:PHE17 3.8 41.3 1.0
C D:ASP33 3.8 40.0 1.0
CA D:ASP33 3.9 44.2 1.0
CG D:ASN35 4.1 54.9 1.0
C D:THR15 4.3 40.4 1.0
OD1 D:ASP33 4.3 55.9 1.0
CA D:PHE17 4.3 39.1 1.0
CD D:LYS171 4.3 72.9 1.0
CG2 D:ILE167 4.4 67.0 1.0
C D:THR16 4.4 40.8 1.0
C D:SER34 4.4 38.6 1.0
CB D:SER170 4.6 66.4 1.0
N D:SER34 4.6 37.5 1.0
CA D:THR16 4.6 40.0 1.0
CB D:ASP33 4.7 46.6 1.0
ND2 D:ASN35 4.9 55.7 1.0
N D:ASP33 4.9 37.6 1.0
O D:ILE167 4.9 71.1 1.0
N D:THR16 5.0 40.1 1.0
CG D:PHE17 5.0 46.4 1.0
CG D:ASP33 5.0 54.3 1.0

Sodium binding site 5 out of 13 in 9qez

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Sodium binding site 5 out of 13 in the Carbonic Anhydrase Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Carbonic Anhydrase Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:62.5
occ:1.00
 O C:HOH353 2.1 51.9 1.0
O E:HOH347 2.2 51.7 1.0
O B:GLY107 2.9 38.3 1.0
O E:HOH349 2.9 50.9 1.0
C B:GLY107 3.8 38.3 1.0
CA B:GLY107 4.0 30.8 1.0
CD1 E:ILE109 4.2 32.8 1.0
O E:HOH343 4.4 52.1 1.0
O E:GLY107 4.7 42.1 1.0
CA B:GLY125 4.9 35.5 1.0
CG1 E:ILE109 5.0 34.0 1.0

Sodium binding site 6 out of 13 in 9qez

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Sodium binding site 6 out of 13 in the Carbonic Anhydrase Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Carbonic Anhydrase Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na202

b:62.7
occ:1.00
 O F:HOH348 2.2 53.9 1.0
CA F:GLY105 3.8 35.0 1.0
CE F:MET106 3.8 37.3 1.0
N F:MET106 4.0 35.3 1.0
O F:HOH344 4.1 47.1 1.0
CD2 F:LEU103 4.2 44.1 1.0
CB F:ALA124 4.4 37.9 1.0
C F:GLY105 4.4 37.9 1.0
CG F:MET106 4.5 35.7 1.0
N F:ALA124 4.7 33.7 1.0
CA F:ALA124 4.9 32.6 1.0
N F:GLY105 4.9 37.4 1.0
SD F:MET106 5.0 42.6 1.0

Sodium binding site 7 out of 13 in 9qez

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Sodium binding site 7 out of 13 in the Carbonic Anhydrase Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Carbonic Anhydrase Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na202

b:63.0
occ:0.50
 OE2 E:GLU32 2.7 50.0 1.0
O E:HOH326 2.8 52.4 1.0
CB E:GLU32 3.4 43.9 1.0
CD E:GLU32 3.5 52.8 1.0
NE2 E:HIS13 3.8 43.3 1.0
CD2 E:HIS13 4.0 45.6 1.0
CG E:GLU32 4.1 45.5 1.0
OE1 E:GLU32 4.5 54.4 1.0
O E:HOH354 4.5 58.1 1.0
N E:GLU32 4.5 40.0 1.0
CA E:GLU32 4.6 43.5 1.0
CE1 E:HIS13 4.8 48.9 1.0
O E:HOH348 4.8 55.1 1.0
CG E:HIS13 5.0 45.9 1.0

Sodium binding site 8 out of 13 in 9qez

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Sodium binding site 8 out of 13 in the Carbonic Anhydrase Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Carbonic Anhydrase Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na203

b:55.6
occ:1.00
 N E:ALA124 3.1 38.5 1.0
CB E:ALA124 3.7 39.0 1.0
CA E:GLY123 3.8 41.1 1.0
C E:GLY123 4.0 37.9 1.0
CA E:ALA124 4.0 37.0 1.0
CD1 C:LEU111 4.1 37.9 1.0
O E:HOH350 4.1 51.0 1.0
O E:HOH339 4.3 53.9 1.0
O C:HOH352 4.5 42.1 1.0

Sodium binding site 9 out of 13 in 9qez

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Sodium binding site 9 out of 13 in the Carbonic Anhydrase Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Carbonic Anhydrase Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:56.0
occ:1.00
 O C:HOH340 2.9 42.5 1.0
O C:ILE81 3.0 38.2 1.0
CE C:LYS50 3.0 53.1 1.0
CD C:LYS50 3.4 58.5 1.0
N C:GLY52 3.7 37.4 1.0
CA C:GLY52 3.8 34.7 1.0
C C:ILE81 3.9 38.8 1.0
CA C:GLY82 4.0 38.3 1.0
C C:ILE51 4.2 37.1 1.0
CG C:LYS50 4.3 47.4 1.0
N C:GLY82 4.3 40.2 1.0
CG2 C:ILE80 4.4 41.9 1.0
NZ C:LYS50 4.4 57.8 1.0
O C:LYS50 4.4 36.6 1.0
C C:GLY82 4.6 40.9 1.0
C C:LYS50 4.6 33.3 1.0
N C:ILE81 4.7 38.9 1.0
CA C:ILE51 4.7 36.1 1.0
O C:ILE51 4.7 37.8 1.0
N C:ILE51 4.8 33.1 1.0
O C:GLY82 4.8 40.3 1.0
CB C:LYS50 4.8 35.7 1.0
O C:HOH336 4.8 51.4 1.0
CA C:ILE81 5.0 38.0 1.0

Sodium binding site 10 out of 13 in 9qez

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Sodium binding site 10 out of 13 in the Carbonic Anhydrase Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Carbonic Anhydrase Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:47.1
occ:1.00
 CH2 L:TRP1 2.7 46.9 1.0
CZ3 L:TRP1 3.0 46.6 1.0
O A:ALA124 3.1 33.6 1.0
N A:GLY142 3.1 39.2 1.0
O A:GLY125 3.2 36.1 1.0
CA A:GLY142 3.3 38.3 1.0
OG A:SER126 3.3 37.1 1.0
C A:GLY125 3.4 37.2 1.0
N A:SER126 3.6 33.4 1.0
CA A:SER126 3.6 39.0 1.0
C A:GLY142 3.7 40.1 1.0
CZ2 L:TRP1 3.9 41.0 1.0
O A:GLY142 4.0 38.6 1.0
CB A:SER126 4.0 36.4 1.0
CD2 F:LEU127 4.1 42.7 1.0
C A:ALA124 4.2 38.1 1.0
CA A:GLY125 4.2 32.5 1.0
C A:MET141 4.3 42.4 1.0
N A:SER143 4.4 44.4 1.0
CE3 L:TRP1 4.4 48.3 1.0
CB A:MET141 4.6 37.4 1.0
O A:GLY123 4.6 33.4 1.0
N A:GLY125 4.6 33.3 1.0
O F:HOH316 4.6 43.4 1.0
OG F:SER143 4.7 45.7 1.0
CA A:MET141 4.8 40.6 1.0
C A:SER126 5.0 34.6 1.0
C A:GLY123 5.0 37.5 1.0

Reference:

C.S.Bodourian, M.Imran, N.D.Georgakis, A.C.Papageorgiou, N.E.Labrou. Structural and Functional Characterization of A Metagenomically Derived Gamma-Type Carbonic Anhydrase and Its Engineering Into A Hyperthermostable Esterase. Protein Sci. V. 34 70396 2025.
ISSN: ESSN 1469-896X
PubMed: 41294346
DOI: 10.1002/PRO.70396
Page generated: Sun Dec 14 18:42:09 2025

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