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Calcium in PDB 4y7e: Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus with Mannohexaose

Enzymatic activity of Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus with Mannohexaose

All present enzymatic activity of Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus with Mannohexaose:
3.2.1.4;

Protein crystallography data

The structure of Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus with Mannohexaose, PDB code: 4y7e was solved by Y.Kumagai, K.Yamashita, M.Okuyama, T.Hatanaka, M.Yao, A.Kimura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.46 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.709, 100.706, 104.737, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 17.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus with Mannohexaose (pdb code 4y7e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus with Mannohexaose, PDB code: 4y7e:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4y7e

Go back to Calcium Binding Sites List in 4y7e
Calcium binding site 1 out of 5 in the Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus with Mannohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus with Mannohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca417

b:12.2
occ:0.75
 OD1 A:ASP250 2.4 10.9 1.0
O A:HOH695 2.4 24.1 1.0
OE2 A:GLU254 2.4 23.0 1.0
OE1 A:GLU254 2.4 19.9 1.0
O A:HOH799 2.4 37.0 1.0
O A:HOH688 2.4 19.9 1.0
O A:VAL248 2.4 10.8 1.0
CD A:GLU254 2.7 21.9 1.0
CG A:ASP250 3.4 11.1 1.0
C A:VAL248 3.6 9.5 1.0
OD2 A:ASP250 3.9 14.8 1.0
N A:ASP250 4.2 8.0 1.0
CA A:VAL248 4.2 9.4 1.0
CG A:GLU254 4.2 18.3 1.0
O A:HOH540 4.3 23.2 1.0
O A:SER247 4.3 10.7 0.7
O A:SER247 4.4 10.7 0.3
CB A:ASP250 4.6 9.3 1.0
O A:HOH890 4.6 48.7 1.0
N A:PHE249 4.6 7.8 1.0
CG1 A:VAL248 4.8 12.0 1.0
CA A:ASP250 4.8 8.4 1.0
O A:HOH780 4.8 28.6 1.0
O A:HOH597 4.9 34.7 1.0
N A:THR251 4.9 9.0 1.0
OG1 A:THR251 4.9 11.5 1.0
CA A:PHE249 5.0 7.2 1.0

Calcium binding site 2 out of 5 in 4y7e

Go back to Calcium Binding Sites List in 4y7e
Calcium binding site 2 out of 5 in the Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus with Mannohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus with Mannohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca418

b:10.1
occ:1.00
 O A:GLY276 2.4 10.6 1.0
OD1 A:ASP283 2.4 9.9 1.0
OE1 A:GLU286 2.4 11.7 1.0
O A:HOH541 2.4 14.6 1.0
O A:HOH783 2.4 11.5 1.0
O A:PRO284 2.4 9.6 1.0
O A:HOH560 2.5 14.7 1.0
C A:GLY276 3.3 9.0 1.0
CG A:ASP283 3.4 10.7 1.0
CD A:GLU286 3.4 11.8 1.0
C A:PRO284 3.6 10.3 1.0
OE2 A:GLU286 3.7 13.9 1.0
OD2 A:ASP283 3.8 12.8 1.0
CA A:GLY276 3.9 12.9 1.0
N A:PRO284 4.2 8.6 1.0
N A:PRO277 4.3 8.8 1.0
C A:ASP283 4.4 9.3 1.0
CA A:PRO284 4.4 8.1 1.0
CD A:PRO284 4.4 8.5 1.0
O A:HOH523 4.5 12.3 1.0
CA A:PRO277 4.5 10.6 1.0
N A:GLU286 4.5 9.4 1.0
N A:ASP285 4.6 9.0 1.0
CD A:PRO278 4.6 9.6 1.0
CB A:ASP283 4.7 11.3 1.0
C A:PRO277 4.7 9.8 1.0
CB A:PRO284 4.7 7.6 1.0
O A:ASP283 4.7 9.8 1.0
O A:HOH825 4.7 28.1 1.0
CA A:ASP285 4.8 8.2 1.0
N A:PRO278 4.8 9.4 1.0
CA A:ASP283 4.8 9.9 1.0
CG A:GLU286 4.8 8.6 1.0

Calcium binding site 3 out of 5 in 4y7e

Go back to Calcium Binding Sites List in 4y7e
Calcium binding site 3 out of 5 in the Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus with Mannohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus with Mannohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca409

b:12.6
occ:1.00
 OD1 B:ASP283 2.3 10.5 1.0
O B:GLY276 2.4 10.2 0.6
O B:HOH770 2.4 16.3 1.0
O B:PRO284 2.4 10.5 1.0
O B:HOH534 2.4 13.6 1.0
OE1 B:GLU286 2.4 14.6 1.0
O B:GLY276 2.4 12.8 0.4
O B:HOH568 2.4 19.2 1.0
C B:GLY276 3.2 7.9 0.6
CG B:ASP283 3.4 11.5 1.0
CD B:GLU286 3.4 14.2 1.0
C B:PRO284 3.6 8.4 1.0
C B:GLY276 3.6 12.2 0.4
OE2 B:GLU286 3.6 16.1 1.0
OD2 B:ASP283 3.8 14.3 1.0
CA B:GLY276 3.8 10.3 0.6
N B:PRO277 4.1 10.0 0.6
N B:PRO284 4.2 8.6 1.0
CA B:PRO277 4.3 10.0 0.6
CA B:PRO277 4.3 10.0 0.4
C B:ASP283 4.3 10.1 1.0
CA B:PRO284 4.4 8.0 1.0
N B:PRO277 4.4 10.3 0.4
O B:HOH540 4.4 11.1 1.0
CD B:PRO284 4.4 9.5 1.0
N B:GLY276 4.5 9.3 0.4
N B:GLU286 4.5 10.8 1.0
C B:PRO277 4.6 11.1 0.4
C B:PRO277 4.6 11.3 0.6
CD B:PRO278 4.6 10.3 1.0
CB B:ASP283 4.6 11.4 1.0
N B:ASP285 4.6 8.2 1.0
CA B:GLY276 4.6 11.4 0.4
CB B:PRO284 4.7 9.4 1.0
O B:ASP283 4.7 11.0 1.0
N B:PRO278 4.7 9.9 1.0
CA B:ASP285 4.8 9.4 1.0
CA B:ASP283 4.8 11.0 1.0
CG B:GLU286 4.8 9.6 1.0

Calcium binding site 4 out of 5 in 4y7e

Go back to Calcium Binding Sites List in 4y7e
Calcium binding site 4 out of 5 in the Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus with Mannohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus with Mannohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca410

b:14.0
occ:0.75
 OD1 B:ASP250 2.4 15.1 1.0
OE2 B:GLU254 2.4 20.6 1.0
O B:HOH788 2.4 32.1 1.0
OE1 B:GLU254 2.4 19.3 1.0
O B:VAL248 2.4 12.6 1.0
O B:HOH633 2.4 19.4 1.0
O B:HOH728 2.4 26.2 1.0
CD B:GLU254 2.7 22.1 1.0
CG B:ASP250 3.4 14.9 1.0
C B:VAL248 3.5 11.0 1.0
OD2 B:ASP250 4.0 16.9 1.0
N B:ASP250 4.2 11.0 1.0
CA B:VAL248 4.2 11.9 1.0
CG B:GLU254 4.3 18.7 1.0
O B:SER247 4.3 12.1 0.5
O B:SER247 4.3 12.2 0.5
O B:HOH591 4.5 36.1 1.0
CB B:ASP250 4.6 13.4 1.0
N B:PHE249 4.6 9.7 1.0
O3 B:GOL404 4.6 33.5 1.0
O B:HOH727 4.7 36.9 1.0
CG1 B:VAL248 4.8 11.9 1.0
CA B:ASP250 4.8 10.6 1.0
CA B:PHE249 4.9 8.8 1.0
CG2 B:THR251 4.9 16.8 1.0
N B:THR251 5.0 12.1 1.0
O B:HOH778 5.0 36.0 1.0

Calcium binding site 5 out of 5 in 4y7e

Go back to Calcium Binding Sites List in 4y7e
Calcium binding site 5 out of 5 in the Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus with Mannohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Beta-Mannanase From Streptomyces Thermolilacinus with Mannohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca411

b:42.4
occ:0.58
 O B:HOH710 2.4 28.4 1.0
O A:HOH852 2.4 30.7 1.0
O B:HOH627 2.4 20.2 1.0
NZ B:LYS198 3.8 13.2 1.0
O B:HOH814 4.0 32.8 1.0
OD2 B:ASP151 4.2 13.4 1.0
NZ A:LYS350 4.6 36.3 1.0
OD1 B:ASP151 4.9 10.6 1.0
O2 B:GOL403 5.0 13.6 1.0
C2 B:GOL403 5.0 18.6 1.0

Reference:

Y.Kumagai, K.Yamashita, T.Tagami, M.Uraji, K.Wan, M.Okuyama, M.Yao, A.Kimura, T.Hatanaka. The Loop Structure of Actinomycete Glycoside Hydrolase Family 5 Mannanases Governs Substrate Recognition Febs J. V. 282 4001 2015.
ISSN: ISSN 1742-464X
PubMed: 26257335
DOI: 10.1111/FEBS.13401
Page generated: Wed Jul 9 03:03:39 2025

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