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Sodium in PDB 4mb3: Crystal Structure of E153Q Mutant of Cold-Adapted Chitinase From Moritella Marina

Enzymatic activity of Crystal Structure of E153Q Mutant of Cold-Adapted Chitinase From Moritella Marina

All present enzymatic activity of Crystal Structure of E153Q Mutant of Cold-Adapted Chitinase From Moritella Marina:
3.2.1.14;

Protein crystallography data

The structure of Crystal Structure of E153Q Mutant of Cold-Adapted Chitinase From Moritella Marina, PDB code: 4mb3 was solved by P.H.Malecki, C.E.Vorgias, W.Rypniewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.44 / 1.55
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 67.657, 67.657, 255.643, 90.00, 90.00, 120.00
R / Rfree (%) 14.1 / 18.3

Other elements in 4mb3:

The structure of Crystal Structure of E153Q Mutant of Cold-Adapted Chitinase From Moritella Marina also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of E153Q Mutant of Cold-Adapted Chitinase From Moritella Marina (pdb code 4mb3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of E153Q Mutant of Cold-Adapted Chitinase From Moritella Marina, PDB code: 4mb3:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4mb3

Go back to Sodium Binding Sites List in 4mb3
Sodium binding site 1 out of 4 in the Crystal Structure of E153Q Mutant of Cold-Adapted Chitinase From Moritella Marina


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of E153Q Mutant of Cold-Adapted Chitinase From Moritella Marina within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:17.1
occ:1.00
 OD1 A:ASN105 2.3 18.1 1.0
OD1 A:ASP146 2.3 17.0 1.0
O A:GLY144 2.3 18.2 1.0
O A:HOH717 2.4 19.8 1.0
O A:THR24 2.6 19.7 1.0
CG A:ASN105 3.1 18.6 1.0
CG A:ASP146 3.2 14.2 1.0
C A:THR24 3.4 25.7 1.0
C A:GLY144 3.4 15.1 1.0
ND2 A:ASN105 3.5 17.8 1.0
OD2 A:ASP146 3.6 16.2 1.0
O A:HOH742 3.8 18.6 1.0
N A:ILE25 3.9 25.0 1.0
CA A:ILE25 3.9 19.5 1.0
O A:PHE145 4.0 17.6 1.0
C A:PHE145 4.0 15.4 1.0
CA A:GLY144 4.1 15.4 1.0
O A:GLY23 4.1 33.8 1.0
C A:GLY23 4.2 30.9 1.0
N A:THR26 4.2 18.5 1.0
N A:THR24 4.3 30.9 1.0
O A:HOH743 4.3 20.1 1.0
N A:ASP146 4.3 15.3 1.0
CA A:THR24 4.4 27.4 1.0
OG1 A:THR26 4.4 21.2 1.0
CB A:ASN105 4.4 17.0 1.0
N A:PHE145 4.4 17.2 1.0
CB A:ASP146 4.4 14.6 1.0
CA A:ASP146 4.5 16.0 1.0
C A:ILE25 4.6 19.7 1.0
CA A:PHE145 4.6 14.9 1.0
CB A:THR26 4.8 20.7 1.0
CG1 A:ILE25 4.9 26.5 1.0
CA A:GLY23 5.0 29.6 1.0
CG2 A:ILE101 5.0 15.1 1.0

Sodium binding site 2 out of 4 in 4mb3

Go back to Sodium Binding Sites List in 4mb3
Sodium binding site 2 out of 4 in the Crystal Structure of E153Q Mutant of Cold-Adapted Chitinase From Moritella Marina


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of E153Q Mutant of Cold-Adapted Chitinase From Moritella Marina within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:38.6
occ:1.00
 O A:HOH740 2.2 36.6 1.0
O A:HOH1197 2.2 43.9 1.0
O A:LYS495 2.3 25.8 1.0
O A:HOH1521 2.3 50.8 1.0
O A:HOH920 2.4 41.0 1.0
O A:HOH765 2.5 33.2 1.0
C A:LYS495 3.4 22.4 1.0
OD1 A:ASP494 3.9 32.6 1.0
OD1 A:ASP433 4.0 25.8 1.0
CA A:ARG496 4.2 21.9 1.0
N A:ARG496 4.2 21.0 1.0
N A:LYS495 4.4 24.3 1.0
OD2 A:ASP494 4.4 37.0 1.0
CA A:LYS495 4.4 25.6 1.0
O A:ILE431 4.4 31.6 1.0
CG A:ASP494 4.4 31.4 1.0
O A:HOH1145 4.6 34.6 1.0
CB A:LYS495 4.8 31.4 1.0
CG2 A:ILE431 4.8 29.1 1.0
CG A:ASP433 4.9 28.9 1.0

Sodium binding site 3 out of 4 in 4mb3

Go back to Sodium Binding Sites List in 4mb3
Sodium binding site 3 out of 4 in the Crystal Structure of E153Q Mutant of Cold-Adapted Chitinase From Moritella Marina


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of E153Q Mutant of Cold-Adapted Chitinase From Moritella Marina within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:34.2
occ:1.00
 O A:HOH1500 2.3 39.1 1.0
O A:HOH1333 2.4 50.6 1.0
O A:HOH799 2.4 27.8 1.0
O A:HOH800 2.4 36.7 1.0
O A:HOH707 2.4 25.9 1.0
O A:ALA241 2.4 28.4 1.0
C A:ALA241 3.2 23.1 1.0
O A:HOH874 3.6 44.0 1.0
O A:HOH1497 3.7 46.7 1.0
CA A:ALA241 3.9 22.4 1.0
N A:LEU242 4.1 20.3 1.0
O A:HOH1348 4.1 46.3 1.0
OD1 A:ASP290 4.2 21.9 1.0
O A:ASP240 4.2 27.9 1.0
O A:HOH718 4.3 35.6 1.0
O A:HOH770 4.3 51.3 1.0
OD2 A:ASP290 4.4 23.7 1.0
O A:HOH1398 4.4 43.0 1.0
O A:HOH1494 4.4 55.3 1.0
CA A:LEU242 4.4 21.1 1.0
N A:LYS243 4.6 18.7 1.0
CG A:ASP290 4.7 19.5 1.0
OE1 A:GLU245 4.7 26.0 1.0
C A:LEU242 4.9 18.1 1.0
N A:ALA241 4.9 20.8 1.0
CB A:ALA241 4.9 24.5 1.0
O A:HOH1347 5.0 50.2 1.0
C A:ASP240 5.0 22.4 1.0

Sodium binding site 4 out of 4 in 4mb3

Go back to Sodium Binding Sites List in 4mb3
Sodium binding site 4 out of 4 in the Crystal Structure of E153Q Mutant of Cold-Adapted Chitinase From Moritella Marina


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of E153Q Mutant of Cold-Adapted Chitinase From Moritella Marina within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:26.3
occ:0.69
 O A:HOH1261 2.2 23.4 1.0
O A:HOH1260 2.3 24.5 1.0
O A:HOH1086 2.3 33.9 1.0
OH A:TYR220 2.4 24.9 1.0
OE1 A:GLN218 3.0 19.1 1.0
CD A:GLN218 3.4 14.7 1.0
CZ A:TYR220 3.5 20.7 1.0
O A:HOH855 3.5 25.2 1.0
CE1 A:TYR220 3.6 17.9 1.0
CB A:TRP311 3.7 17.3 1.0
NE2 A:GLN218 3.8 16.6 1.0
CE3 A:TRP311 3.8 13.9 1.0
CG A:TRP311 3.9 15.8 1.0
CD2 A:TRP311 3.9 14.6 1.0
CG A:GLN218 4.2 12.9 1.0
O A:HOH806 4.3 48.2 1.0
O A:HOH1379 4.4 39.9 1.0
OE1 A:GLN153 4.6 22.6 1.0
CZ3 A:TRP311 4.7 16.8 1.0
CE2 A:TYR220 4.7 17.6 1.0
O A:HOH864 4.7 19.9 1.0
OD2 A:ASP151 4.8 19.6 1.0
CD1 A:TRP311 4.8 14.9 1.0
CE2 A:TRP311 4.8 14.5 1.0
CD1 A:TYR220 5.0 15.5 1.0

Reference:

P.H.Malecki, C.E.Vorgias, M.V.Petoukhov, D.I.Svergun, W.Rypniewski. Crystal Structures of Substrate-Bound Chitinase From the Psychrophilic Bacterium Moritella Marina and Its Structure in Solution Acta Crystallogr.,Sect.D V. 70 676 2014.
ISSN: ISSN 0907-4449
PubMed: 24598737
DOI: 10.1107/S1399004713032264
Page generated: Mon Oct 7 16:58:46 2024

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