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Sodium in PDB 4zh5: Crystal Structure of Endoglucanase From Perinereis Brevicirris with Cellobiose

Enzymatic activity of Crystal Structure of Endoglucanase From Perinereis Brevicirris with Cellobiose

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

Protein crystallography data

The structure of Crystal Structure of Endoglucanase From Perinereis Brevicirris with Cellobiose, PDB code: 4zh5 was solved by R.S.Fewings, A.Swiderska, J.Sanchez-Weatherby, T.-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) 16.98 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.150, 108.170, 112.680, 90.00, 90.00, 90.00
R / Rfree (%) 11.5 / 14.8

Other elements in 4zh5:

The structure of Crystal Structure of Endoglucanase From Perinereis Brevicirris with Cellobiose 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 with Cellobiose (pdb code 4zh5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Endoglucanase From Perinereis Brevicirris with Cellobiose, PDB code: 4zh5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4zh5

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Sodium binding site 1 out of 5 in the Crystal Structure of Endoglucanase From Perinereis Brevicirris with Cellobiose


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 with Cellobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:34.4
occ:1.00
 O A:HOH990 2.0 34.3 1.0
O B:HOH820 2.3 20.5 1.0
O A:GLN246 2.4 14.9 1.0
O A:HOH1033 2.4 26.1 1.0
O A:HOH1149 2.5 36.7 1.0
O A:HOH945 3.3 21.1 1.0
C A:GLN246 3.6 10.4 1.0
O A:HOH902 3.9 20.6 1.0
O B:HOH676 3.9 32.3 1.0
CA A:GLN246 4.4 11.6 1.0
CB A:GLN246 4.4 16.0 1.0
OE2 A:GLU258 4.5 18.9 1.0
N A:GLY247 4.5 11.1 1.0
N A:GLN246 4.5 10.4 1.0
CA A:GLY247 4.5 12.0 1.0
OE2 B:GLU202 4.6 14.7 1.0
O A:ARG248 4.6 8.4 1.0
C A:GLY247 4.6 11.5 1.0
O A:HOH948 4.7 39.9 1.0
O A:GLY247 5.0 13.5 1.0
N A:ARG248 5.0 8.6 1.0

Sodium binding site 2 out of 5 in 4zh5

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Sodium binding site 2 out of 5 in the Crystal Structure of Endoglucanase From Perinereis Brevicirris with Cellobiose


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 with Cellobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:29.8
occ:1.00
 O A:HOH1062 2.1 36.1 1.0
O A:HOH935 2.4 28.0 1.0
O A:HOH1093 2.5 50.6 1.0
O A:GLY288 2.6 10.6 1.0
O A:HOH969 2.8 42.6 1.0
O A:GLY287 2.8 10.5 1.0
C A:GLY288 3.4 7.4 1.0
C A:GLY287 3.4 8.5 1.0
CA A:GLY288 3.8 7.2 1.0
N A:GLY288 3.9 7.5 1.0
O A:HOH995 3.9 20.9 1.0
O A:HOH1145 4.0 55.3 1.0
O A:HOH631 4.1 19.6 1.0
CA A:GLY287 4.3 8.6 1.0
N A:ASP289 4.4 7.1 1.0
OD1 A:ASP289 4.5 11.5 1.0
CA A:ASP289 4.8 7.5 1.0

Sodium binding site 3 out of 5 in 4zh5

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Sodium binding site 3 out of 5 in the Crystal Structure of Endoglucanase From Perinereis Brevicirris with Cellobiose


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 with Cellobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:16.7
occ:1.00
 O A:HOH1109 2.7 79.0 1.0
N A:GLN328 3.0 7.0 1.0
O A:HOH657 3.2 18.5 1.0
N A:SER327 3.3 7.0 1.0
CB A:GLN328 3.6 7.6 1.0
CB A:SER327 3.6 7.6 0.5
O A:LEU325 3.6 7.7 1.0
C A:LEU325 3.7 6.8 1.0
CB A:SER327 3.7 10.6 0.5
CA A:SER327 3.7 7.4 0.5
CA A:SER327 3.8 7.8 0.5
C A:SER327 3.8 7.1 1.0
CA A:GLN328 3.8 7.1 1.0
N A:THR326 3.9 7.9 1.0
C A:THR326 4.2 7.1 1.0
CA A:LEU325 4.2 6.8 1.0
OG A:SER327 4.3 8.8 0.5
CA A:THR326 4.6 8.5 1.0
OE1 A:GLN328 4.7 11.3 1.0
OG A:SER327 4.7 16.6 0.5
CB A:LEU325 4.8 7.3 1.0
CG A:GLN328 4.9 7.6 1.0
O A:SER327 5.0 8.0 1.0
C A:GLN328 5.0 6.5 1.0

Sodium binding site 4 out of 5 in 4zh5

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Sodium binding site 4 out of 5 in the Crystal Structure of Endoglucanase From Perinereis Brevicirris with Cellobiose


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 with Cellobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na507

b:33.2
occ:1.00
 O B:HOH605 2.1 31.0 1.0
OE2 A:GLU202 2.8 16.0 1.0
O B:ARG248 2.9 9.0 1.0
O B:HOH957 3.1 23.9 1.0
O B:GLN246 3.3 14.3 1.0
O B:HOH994 3.3 30.1 1.0
O A:HOH693 3.4 30.2 1.0
CD A:GLU202 3.7 13.0 1.0
C B:ARG248 3.7 7.8 1.0
O A:HOH750 3.7 29.2 1.0
N B:ARG248 3.8 9.0 1.0
OE1 A:GLU202 3.9 16.1 1.0
C B:GLY247 4.0 10.4 1.0
CA B:GLY247 4.3 12.2 1.0
O B:HOH841 4.4 16.2 1.0
O A:HOH903 4.4 13.7 1.0
C B:GLN246 4.4 12.2 1.0
CA B:ARG248 4.4 8.4 1.0
O B:HOH810 4.4 21.0 1.0
N B:PRO249 4.5 7.7 1.0
O B:GLY247 4.6 12.0 1.0
CA B:PRO249 4.7 8.7 1.0
N B:GLY247 4.8 11.6 1.0
CG A:GLU202 4.9 12.2 1.0

Sodium binding site 5 out of 5 in 4zh5

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


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 with Cellobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na505

b:41.5
occ:1.00
 OD1 B:ASP47 2.6 16.1 1.0
O B:HOH1065 3.2 20.8 1.0
N B:ASP47 3.2 17.5 1.0
C B:ASP46 3.4 19.9 1.0
CB B:ASP46 3.6 24.2 1.0
O B:HOH839 3.6 40.8 1.0
N B:ASP46 3.7 19.7 1.0
CA B:ASP46 3.7 21.3 1.0
CD B:ARG142 3.7 16.0 1.0
CG B:ASP47 3.7 16.4 1.0
CA B:ALA44 3.8 17.1 1.0
CA B:ASP47 3.8 16.7 1.0
NE B:ARG142 3.9 16.0 1.0
C B:ALA44 4.0 18.3 1.0
O B:ASP46 4.0 22.5 1.0
O B:ALA44 4.1 19.2 1.0
CB B:ALA44 4.2 17.8 1.0
CB B:ASP47 4.3 15.2 1.0
O B:HOH780 4.4 26.3 1.0
CB B:ARG142 4.5 16.2 1.0
N B:LEU45 4.5 21.9 1.0
CG B:ARG142 4.5 16.0 1.0
CG B:ASP46 4.7 35.1 1.0
O B:HOH851 4.7 38.7 1.0
OD2 B:ASP47 4.8 15.6 1.0
OD2 B:ASP46 4.8 43.2 1.0
C B:LEU45 4.8 20.8 1.0

Reference:

R.S.Fewings, R.S.Fewings, A.Swiderska, J.Sanchez-Weatherby, T.-M.Sorensen, K.M.Schnorr, G.G.Kneale, J.E.Mcgeehan. N/A N/A.
Page generated: Tue Dec 15 10:07:21 2020

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