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: Sat Dec 12 05:13:07 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy