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Sodium in PDB 3t9g: The Crystal Structure of Family 3 Pectate Lyase From Caldicellulosiruptor Bescii

Enzymatic activity of The Crystal Structure of Family 3 Pectate Lyase From Caldicellulosiruptor Bescii

All present enzymatic activity of The Crystal Structure of Family 3 Pectate Lyase From Caldicellulosiruptor Bescii:
4.2.2.2;

Protein crystallography data

The structure of The Crystal Structure of Family 3 Pectate Lyase From Caldicellulosiruptor Bescii, PDB code: 3t9g was solved by P.M.Alahuhta, V.V.Lunin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 36.514, 146.685, 162.159, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 17.8

Other elements in 3t9g:

The structure of The Crystal Structure of Family 3 Pectate Lyase From Caldicellulosiruptor Bescii also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of Family 3 Pectate Lyase From Caldicellulosiruptor Bescii (pdb code 3t9g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the The Crystal Structure of Family 3 Pectate Lyase From Caldicellulosiruptor Bescii, PDB code: 3t9g:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3t9g

Go back to Sodium Binding Sites List in 3t9g
Sodium binding site 1 out of 4 in the The Crystal Structure of Family 3 Pectate Lyase From Caldicellulosiruptor Bescii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Family 3 Pectate Lyase From Caldicellulosiruptor Bescii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:15.3
occ:0.70
 OD1 A:ASP85 1.5 6.4 0.3
O A:HOH398 2.3 18.1 1.0
OD1 A:ASP64 2.4 17.5 1.0
O A:HOH374 2.4 26.4 1.0
OD2 A:ASP85 2.5 26.7 0.7
OD2 A:ASP64 2.7 17.7 1.0
CG A:ASP85 2.7 8.4 0.3
OD1 A:ASP85 2.7 27.4 0.7
CG A:ASP64 2.8 17.6 1.0
CG A:ASP85 2.9 20.3 0.7
OE2 A:GLU84 3.0 27.4 1.0
CD A:GLU84 3.2 24.3 1.0
CB A:ASP85 3.6 7.2 0.3
OD2 A:ASP85 3.6 6.0 0.3
O A:HOH430 3.7 34.5 1.0
CG A:GLU84 3.7 19.9 1.0
OE1 A:GLU84 3.8 23.7 1.0
OG1 A:THR88 4.2 10.7 1.0
CB A:GLU84 4.3 13.6 1.0
CB A:ASP64 4.3 12.7 1.0
CB A:ASP85 4.3 14.8 0.7
N A:ASP85 4.3 9.8 0.3
N A:ASP85 4.5 12.5 0.7
CA A:ASP85 4.6 8.0 0.3
O A:HOH547 4.7 39.6 1.0
C A:GLU84 4.7 11.1 1.0
O A:HOH477 4.8 29.0 1.0
O A:HOH353 4.8 12.7 1.0
O A:HOH478 4.8 25.5 1.0
CA A:ASP85 5.0 12.5 0.7
CA A:ASP64 5.0 10.8 1.0

Sodium binding site 2 out of 4 in 3t9g

Go back to Sodium Binding Sites List in 3t9g
Sodium binding site 2 out of 4 in the The Crystal Structure of Family 3 Pectate Lyase From Caldicellulosiruptor Bescii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Family 3 Pectate Lyase From Caldicellulosiruptor Bescii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na209

b:9.7
occ:0.70
 OD1 B:ASP85 1.8 5.6 0.3
O B:HOH364 2.0 20.5 1.0
OE1 B:GLU84 2.1 11.4 0.3
OD1 B:ASP64 2.3 23.5 1.0
O B:HOH431 2.4 9.3 0.5
OD1 B:ASP85 2.6 22.7 0.7
OD2 B:ASP85 2.7 19.4 0.7
CG B:ASP85 2.9 9.6 0.3
CG B:ASP64 2.9 16.2 1.0
CG B:ASP85 3.0 16.1 0.7
OD2 B:ASP64 3.2 22.8 1.0
CD B:GLU84 3.2 10.0 0.3
OE2 B:GLU84 3.5 22.9 0.7
CD B:GLU84 3.6 21.9 0.7
CB B:ASP85 3.7 6.7 0.3
OD2 B:ASP85 3.8 7.9 0.3
OG1 B:THR88 3.8 13.0 1.0
OE2 B:GLU84 3.9 12.2 0.3
O B:HOH527 3.9 28.1 0.5
CG B:GLU84 4.0 14.7 0.7
OE1 B:GLU84 4.1 12.9 0.7
O B:HOH348 4.3 17.9 1.0
CG B:GLU84 4.4 4.8 0.3
CB B:ASP64 4.5 11.2 1.0
CB B:ASP85 4.5 9.5 0.7
O B:HOH484 4.5 17.8 0.7
CB B:GLU84 4.5 7.0 0.3
O B:HOH309 4.5 12.9 1.0
CB B:GLU84 4.5 10.7 0.7
O B:HOH549 4.6 8.3 0.3
N B:ASP85 4.6 7.3 0.3
N B:ASP85 4.7 8.8 0.7
CA B:ASP85 4.8 6.3 0.3
O B:ASP64 4.8 10.5 1.0
OE1 B:GLN111 4.8 6.9 0.3
NE2 B:HIS67 4.8 11.6 1.0
CB B:THR88 5.0 7.7 1.0

Sodium binding site 3 out of 4 in 3t9g

Go back to Sodium Binding Sites List in 3t9g
Sodium binding site 3 out of 4 in the The Crystal Structure of Family 3 Pectate Lyase From Caldicellulosiruptor Bescii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of Family 3 Pectate Lyase From Caldicellulosiruptor Bescii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na210

b:25.6
occ:1.00
 O B:HOH482 2.1 7.1 0.5
O B:GLY136 2.8 11.2 1.0
OD1 B:ASN135 3.0 13.3 1.0
N B:GLY136 3.4 10.0 1.0
C B:GLY136 3.5 9.8 1.0
CA B:GLY136 3.6 10.1 1.0
CG B:ASN135 3.7 9.6 1.0
O B:HOH482 4.0 21.0 0.5
C B:ASN135 4.1 9.9 1.0
ND2 B:ASN135 4.2 10.6 1.0
O B:HOH409 4.3 17.1 1.0
O B:ACT215 4.3 31.4 0.5
CB B:ASN135 4.7 9.1 1.0
O B:ASN135 4.8 10.3 1.0
CA B:ASN135 4.8 8.5 1.0
N B:ASN137 4.8 10.3 1.0

Sodium binding site 4 out of 4 in 3t9g

Go back to Sodium Binding Sites List in 3t9g
Sodium binding site 4 out of 4 in the The Crystal Structure of Family 3 Pectate Lyase From Caldicellulosiruptor Bescii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of Family 3 Pectate Lyase From Caldicellulosiruptor Bescii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na211

b:22.5
occ:1.00
 O B:HOH550 2.2 30.5 1.0
O B:HOH342 3.0 18.0 1.0
O B:HOH347 3.1 20.0 1.0
N B:GLN37 3.3 7.5 0.7
N B:GLN37 3.4 7.3 0.3
CB B:SER36 3.7 7.4 1.0
CB B:GLN37 3.9 8.6 0.7
CB B:GLN37 4.0 7.0 0.3
CA B:SER36 4.0 7.9 1.0
CG B:GLN37 4.0 9.7 0.7
CG B:GLN37 4.1 5.8 0.3
C B:SER36 4.2 7.1 1.0
CA B:GLN37 4.2 7.4 0.7
CA B:GLN37 4.2 7.0 0.3
O B:HOH330 4.6 9.3 1.0
OG B:SER36 4.6 8.3 1.0

Reference:

M.Alahuhta, P.Chandrayan, I.Kataeva, M.W.Adams, M.E.Himmel, V.V.Lunin. A 1.5 A Resolution X-Ray Structure of the Catalytic Module of Caldicellulosiruptor Bescii Family 3 Pectate Lyase. Acta Crystallogr.,Sect.F V. 67 1498 2011.
ISSN: ESSN 1744-3091
PubMed: 22139151
DOI: 10.1107/S1744309111038449
Page generated: Tue Dec 15 06:25:58 2020

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