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Sodium in PDB 4zg8: Crystal Structure of Endoglucanase From Perinereis Brevicirris

Enzymatic activity of Crystal Structure of Endoglucanase From Perinereis Brevicirris

All present enzymatic activity of Crystal Structure of Endoglucanase From Perinereis Brevicirris:
3.2.1.4;

Protein crystallography data

The structure of Crystal Structure of Endoglucanase From Perinereis Brevicirris, PDB code: 4zg8 was solved by R.S.Fewings, A.Swiderska, J.Sanchez-Weatherby, T.L.-M.Sorensen, K.M.Schnorr, G.G.Kneale, J.E.Mcgeehan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.41 / 1.39
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.600, 110.340, 113.020, 90.00, 90.00, 90.00
R / Rfree (%) 11 / 14.8

Other elements in 4zg8:

The structure of Crystal Structure of Endoglucanase From Perinereis Brevicirris 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 Crystal Structure of Endoglucanase From Perinereis Brevicirris (pdb code 4zg8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Endoglucanase From Perinereis Brevicirris, PDB code: 4zg8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4zg8

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Sodium binding site 1 out of 6 in the Crystal Structure of Endoglucanase From Perinereis Brevicirris


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 Endoglucanase From Perinereis Brevicirris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:41.8
occ:1.00
 O A:HOH837 2.2 31.2 1.0
O A:GLN246 2.5 17.9 1.0
O A:HOH1041 2.6 43.3 1.0
O A:HOH1144 2.7 46.0 1.0
O B:HOH755 3.0 46.4 1.0
C A:GLN246 3.6 15.2 1.0
O A:HOH952 3.9 25.5 1.0
O A:HOH994 4.1 21.8 1.0
O A:HOH1044 4.2 27.9 1.0
OE2 B:GLU202 4.4 24.5 1.0
N A:GLY247 4.5 16.0 1.0
CA A:GLY247 4.5 17.1 1.0
CA A:GLN246 4.6 14.8 1.0
O A:ARG248 4.6 11.8 1.0
CB A:GLN246 4.6 17.6 1.0
C A:GLY247 4.7 14.5 1.0
N A:GLN246 4.8 12.2 1.0
OE2 A:GLU258 4.9 28.8 1.0
N A:ARG248 4.9 12.2 1.0
O B:HOH680 5.0 24.9 1.0

Sodium binding site 2 out of 6 in 4zg8

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Sodium binding site 2 out of 6 in the Crystal Structure of Endoglucanase From Perinereis Brevicirris


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 Endoglucanase From Perinereis Brevicirris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:33.4
occ:1.00
 O A:HOH1055 2.2 43.7 1.0
O A:HOH1073 2.3 60.2 1.0
O A:GLY288 2.6 14.5 1.0
O A:HOH928 2.6 36.7 1.0
O A:GLY287 2.7 13.1 1.0
O A:HOH772 3.1 41.0 1.0
C A:GLY287 3.4 11.6 1.0
C A:GLY288 3.4 11.2 1.0
CA A:GLY288 3.8 11.3 1.0
N A:GLY288 3.9 12.1 1.0
O A:HOH675 4.4 26.1 1.0
CA A:GLY287 4.4 12.1 1.0
N A:ASP289 4.4 10.5 1.0
OD1 A:ASP289 4.5 17.4 1.0
CA A:ASP289 4.9 11.8 1.0
O A:HOH666 4.9 29.3 1.0

Sodium binding site 3 out of 6 in 4zg8

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Sodium binding site 3 out of 6 in the Crystal Structure of Endoglucanase From Perinereis Brevicirris


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 Endoglucanase From Perinereis Brevicirris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:62.1
occ:1.00
 OD1 A:ASP96 2.7 20.1 0.5
O A:HOH1000 3.3 49.3 1.0
CA A:ASP96 3.8 15.8 0.5
CA A:ASP96 3.8 15.3 0.5
N A:ASP96 3.9 16.7 0.5
N A:ASP96 3.9 16.4 0.5
CG A:ASP96 3.9 20.1 0.5
O A:ASN95 3.9 16.3 1.0
C A:ASN95 3.9 15.4 1.0
CB A:ASN95 4.3 21.4 1.0
CB A:ASP96 4.4 20.0 0.5
O A:HOH796 4.5 29.3 1.0
CB A:ASP96 4.5 17.0 0.5
CB A:GLN99 4.5 18.6 1.0
O A:HOH799 4.8 23.0 1.0
CA A:ASN95 4.8 17.0 1.0
OD1 A:ASP96 4.8 36.1 0.5
OD2 A:ASP96 4.9 23.2 0.5
CG A:GLN99 4.9 27.4 1.0

Sodium binding site 4 out of 6 in 4zg8

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Sodium binding site 4 out of 6 in the Crystal Structure of Endoglucanase From Perinereis Brevicirris


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 Endoglucanase From Perinereis Brevicirris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:43.2
occ:1.00
 O B:HOH606 2.2 38.2 1.0
O B:ARG248 2.8 13.5 1.0
OE2 A:GLU202 2.9 26.6 1.0
O A:HOH848 3.3 32.4 1.0
O A:HOH626 3.3 47.4 1.0
O B:GLN246 3.4 21.8 1.0
O B:HOH965 3.5 33.6 1.0
C B:ARG248 3.6 11.1 1.0
N B:ARG248 3.6 12.1 1.0
CD A:GLU202 3.8 20.4 1.0
O B:HOH999 3.8 41.4 1.0
O B:HOH944 3.9 25.4 1.0
C B:GLY247 3.9 15.4 1.0
CA B:GLY247 4.1 18.5 1.0
OE1 A:GLU202 4.2 26.0 1.0
CA B:ARG248 4.2 11.4 1.0
O B:HOH846 4.3 24.2 1.0
O B:HOH909 4.4 21.3 1.0
C B:GLN246 4.5 19.0 1.0
N B:PRO249 4.5 11.2 1.0
O B:GLY247 4.6 17.7 1.0
CA B:PRO249 4.7 11.2 1.0
N B:GLY247 4.8 17.0 1.0
CG A:GLU202 4.8 18.1 1.0
O A:HOH1114 5.0 43.2 1.0

Sodium binding site 5 out of 6 in 4zg8

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Sodium binding site 5 out of 6 in the Crystal Structure of Endoglucanase From Perinereis Brevicirris


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Endoglucanase From Perinereis Brevicirris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:20.9
occ:1.00
 O A:HOH1011 2.8 21.5 1.0
N A:GLN328 3.0 10.8 1.0
O A:HOH654 3.0 20.8 1.0
N A:SER327 3.4 11.8 1.0
CB A:GLN328 3.6 10.6 1.0
O A:LEU325 3.6 11.6 1.0
C A:LEU325 3.6 11.0 1.0
CB A:SER327 3.7 15.3 0.5
CA A:SER327 3.8 12.3 0.5
CA A:SER327 3.8 11.7 0.5
N A:THR326 3.8 12.0 1.0
C A:SER327 3.8 11.0 1.0
CA A:GLN328 3.9 10.6 1.0
CB A:SER327 3.9 11.5 0.5
CA A:LEU325 4.2 10.9 1.0
C A:THR326 4.2 11.5 1.0
CA A:THR326 4.6 13.2 1.0
OG A:SER327 4.6 14.3 0.5
OE1 A:GLN328 4.6 14.8 1.0
OG A:SER327 4.7 20.6 0.5
CB A:LEU325 4.8 11.8 1.0
CG A:GLN328 4.8 11.0 1.0
O A:HOH637 4.9 18.9 1.0

Sodium binding site 6 out of 6 in 4zg8

Go back to Sodium Binding Sites List in 4zg8
Sodium binding site 6 out of 6 in the Crystal Structure of Endoglucanase From Perinereis Brevicirris


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Endoglucanase From Perinereis Brevicirris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:58.5
occ:1.00
 O B:HOH1058 2.5 34.5 1.0
OD2 B:ASP175 2.8 39.7 1.0
O B:HOH790 3.2 54.1 1.0
OD1 B:ASP175 3.2 34.2 1.0
CG B:ASP175 3.4 30.5 1.0
CB B:TYR178 3.8 22.9 1.0
O B:HOH1012 3.9 36.4 1.0
O B:HOH719 4.0 37.5 1.0
NH1 B:ARG102 4.2 33.0 1.0
N B:TYR178 4.3 25.3 1.0
CA B:TYR178 4.4 21.6 1.0
CD1 B:TYR178 4.4 24.2 1.0
CG B:TYR178 4.4 21.3 1.0
OG B:SER177 4.7 27.7 0.5
O B:HOH924 4.7 36.1 1.0
CB B:ASP175 4.9 30.6 1.0
NH2 B:ARG102 5.0 31.5 1.0

Reference:

R.S.Fewings, R.S.Fewings, A.Swiderska, J.Sanchez-Weatherby, T.L.-M.Sorensen, K.M.Schnorr, G.G.Kneale, J.E.Mcgeehan. N/A N/A.
Page generated: Mon Oct 7 19:40:35 2024

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