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Sodium in PDB 5cgm: Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution

Enzymatic activity of Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution

All present enzymatic activity of Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution:
2.4.99.16;

Protein crystallography data

The structure of Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution, PDB code: 5cgm was solved by V.Mendes, M.Blaszczyk, A.Maranha, N.Empadinhas, T.L.Blundell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.66 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.330, 113.900, 220.500, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 20.3

Other elements in 5cgm:

The structure of Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Sodium atom in the Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution (pdb code 5cgm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 19 binding sites of Sodium where determined in the Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution, PDB code: 5cgm:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 19 in 5cgm

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Sodium binding site 1 out of 19 in the Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na704

b:40.1
occ:1.00
 O A:LEU150 2.7 31.0 1.0
NE A:ARG179 3.0 31.0 1.0
NH1 A:ARG179 3.1 27.9 1.0
C A:LEU150 3.4 33.1 1.0
CZ A:ARG179 3.5 37.0 1.0
CA A:LEU150 3.6 30.6 1.0
CB A:LEU150 3.6 31.1 1.0
CG A:ARG154 3.6 32.1 1.0
CB A:ALA153 3.8 24.7 1.0
CG A:LEU150 3.8 35.1 1.0
NE A:ARG154 4.1 35.4 1.0
N A:ARG154 4.2 22.4 1.0
CD A:ARG179 4.2 30.6 1.0
CG A:ARG179 4.3 34.7 1.0
CD A:ARG154 4.3 33.9 1.0
N A:VAL151 4.6 30.7 1.0
CB A:ARG154 4.7 21.7 1.0
CD2 A:LEU150 4.7 34.4 1.0
C A:ALA153 4.7 25.0 1.0
CA A:ALA153 4.8 23.6 1.0
NH2 A:ARG179 4.8 21.0 1.0
CA A:ARG154 4.8 22.7 1.0
CD1 A:LEU150 4.9 34.5 1.0

Sodium binding site 2 out of 19 in 5cgm

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Sodium binding site 2 out of 19 in the Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na705

b:20.0
occ:1.00
 CA A:SER0 2.7 34.7 1.0
N A:GLU213 3.0 24.5 1.0
O A:HOH839 3.2 20.5 1.0
N A:SER0 3.3 36.3 1.0
CA A:GLY212 3.5 22.7 1.0
C A:SER0 3.6 34.2 1.0
C A:GLY212 3.8 26.2 1.0
CG2 A:VAL10 3.8 19.6 1.0
CB A:GLU213 3.9 27.0 1.0
N A:VAL1 4.0 27.6 1.0
CA A:GLU213 4.0 24.8 1.0
CG2 A:ILE7 4.0 21.9 1.0
CG A:GLU213 4.2 42.0 1.0
CE2 A:TYR215 4.3 23.8 1.0
O A:SER0 4.3 32.5 1.0
CG1 A:VAL1 4.3 30.9 1.0
O A:GLU213 4.4 23.6 1.0
CB A:ILE7 4.5 22.2 1.0
OH A:TYR215 4.5 29.3 1.0
CG2 A:VAL1 4.5 30.3 1.0
C A:GLY-1 4.5 39.0 1.0
CB A:VAL10 4.7 20.1 1.0
C A:GLU213 4.7 24.5 1.0
N A:GLY212 4.9 22.8 1.0
CB A:VAL1 4.9 31.0 1.0
CZ A:TYR215 4.9 30.9 1.0
O A:ILE7 5.0 21.8 1.0
O A:GLY212 5.0 25.2 1.0

Sodium binding site 3 out of 19 in 5cgm

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Sodium binding site 3 out of 19 in the Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na706

b:33.2
occ:1.00
 O A:PRO497 2.6 19.1 1.0
OE1 A:GLU546 2.6 49.0 1.0
N A:TYR547 3.0 19.8 1.0
O A:HOH937 3.2 27.7 1.0
OG A:SER550 3.3 21.4 1.0
CD A:GLU546 3.4 56.4 1.0
CA A:GLU546 3.5 22.5 1.0
CE A:LYS552 3.6 21.9 1.0
CB A:SER550 3.7 17.8 1.0
C A:GLU546 3.7 24.4 1.0
C A:PRO497 3.8 19.3 1.0
CB A:GLU546 3.8 24.3 1.0
CB A:TYR547 3.9 19.3 1.0
CA A:TYR547 3.9 19.2 1.0
O A:TYR547 4.0 22.3 1.0
NZ A:LYS552 4.0 21.9 1.0
CD2 A:TYR547 4.1 18.8 1.0
OE2 A:GLU546 4.1 48.9 1.0
CG A:GLU546 4.2 32.3 1.0
CA A:ASP498 4.3 18.5 1.0
C A:TYR547 4.4 23.7 1.0
CG A:TYR547 4.5 18.7 1.0
N A:ASP498 4.5 17.8 1.0
CA A:SER550 4.7 17.4 1.0
C A:ASP498 4.8 22.0 1.0
O A:HOH1155 4.8 41.7 1.0
CD A:LYS552 4.8 20.0 1.0
N A:GLU546 4.9 22.9 1.0
O A:GLU546 4.9 23.7 1.0
CA A:PRO497 4.9 14.8 1.0
O A:GLU545 4.9 24.8 1.0
O A:HOH897 4.9 26.5 1.0

Sodium binding site 4 out of 19 in 5cgm

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Sodium binding site 4 out of 19 in the Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na707

b:41.6
occ:1.00
 O A:GLY507 2.6 29.7 1.0
N A:GLY510 3.1 24.3 1.0
CA A:GLY510 3.5 23.1 1.0
C A:GLY508 3.5 30.9 1.0
CA A:GLY508 3.6 27.8 1.0
O A:PRO625 3.6 36.9 1.0
N A:PRO509 3.7 26.6 1.0
C A:GLY507 3.7 30.7 1.0
CB A:PRO625 3.8 29.1 1.0
CD A:PRO509 3.9 28.1 1.0
O A:GLY508 4.1 29.9 1.0
N A:GLY508 4.1 28.5 1.0
C A:PRO509 4.2 28.9 1.0
N A:MET511 4.2 19.2 1.0
CE1 A:PHE626 4.2 42.8 1.0
C A:PRO625 4.2 36.1 1.0
CD1 A:PHE626 4.4 42.2 1.0
C A:GLY510 4.4 24.4 1.0
CA A:PRO509 4.4 26.1 1.0
CG A:PRO625 4.5 32.6 1.0
CA A:PRO625 4.6 28.0 1.0
CA A:GLY507 5.0 28.0 1.0

Sodium binding site 5 out of 19 in 5cgm

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Sodium binding site 5 out of 19 in the Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na708

b:42.4
occ:1.00
 O A:HOH1022 2.6 42.4 1.0
O A:LEU548 3.0 21.4 1.0
O A:HOH1005 3.2 33.1 1.0
O A:GLN538 3.2 25.0 1.0
NA A:NA714 3.2 50.0 1.0
N A:LEU548 3.6 21.0 1.0
CD1 A:TYR547 3.7 19.8 1.0
C A:LEU548 3.9 23.5 1.0
CB A:TYR547 4.0 19.3 1.0
CB A:LEU548 4.1 19.8 1.0
CA A:LEU548 4.1 19.7 1.0
C A:GLN538 4.2 25.7 1.0
N A:GLN538 4.2 21.7 1.0
CB A:GLN538 4.2 23.6 1.0
C3 A:PG4719 4.3 45.9 1.0
C A:TYR547 4.3 23.7 1.0
CG A:TYR547 4.4 18.7 1.0
CA A:GLN538 4.4 22.4 1.0
NH1 A:ARG556 4.4 19.8 1.0
CA A:TYR547 4.4 19.2 1.0
CB A:GLU536 4.6 21.7 1.0
CE1 A:TYR547 4.8 18.8 1.0
NH2 A:ARG556 4.8 22.0 1.0
C4 A:PG4719 4.9 43.9 1.0
OE1 A:GLU536 5.0 25.4 1.0

Sodium binding site 6 out of 19 in 5cgm

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Sodium binding site 6 out of 19 in the Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na709

b:39.9
occ:1.00
 OE2 A:GLU27 2.6 28.2 1.0
O A:HOH971 2.6 38.4 1.0
O A:HOH811 3.1 43.6 1.0
CD A:GLU27 3.3 31.8 1.0
NH2 A:ARG225 3.4 23.0 1.0
OE1 A:GLU27 3.6 25.0 1.0
O A:HOH954 3.6 19.2 1.0
CD A:ARG225 3.7 28.5 1.0
NH1 A:ARG591 3.9 17.7 0.5
CB A:LEU590 4.1 30.3 1.0
CD1 A:LEU590 4.2 38.0 1.0
CZ A:ARG591 4.4 36.5 0.5
CB A:ALA485 4.4 21.0 1.0
CZ A:ARG225 4.4 34.1 1.0
CG A:GLU27 4.4 21.7 1.0
NH2 A:ARG591 4.5 25.4 0.5
NE A:ARG225 4.5 24.7 1.0
N A:LEU590 4.6 25.9 1.0
NH2 A:ARG591 4.6 33.0 0.5
CG A:LEU590 4.6 37.4 1.0
OE1 A:GLU589 4.7 34.9 1.0
O A:ALA485 4.7 24.8 1.0
NE A:ARG591 4.8 38.8 0.5
CG A:ARG225 4.9 27.3 1.0
O A:HOH859 4.9 34.1 1.0
N A:ARG591 5.0 21.9 1.0

Sodium binding site 7 out of 19 in 5cgm

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Sodium binding site 7 out of 19 in the Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na710

b:37.4
occ:1.00
 OE1 A:GLU696 2.4 51.1 1.0
OG1 A:THR34 2.8 22.1 1.0
O A:ASP9 2.9 20.5 1.0
CD A:GLU696 3.3 68.8 1.0
N A:THR34 3.4 19.1 1.0
OE2 A:GLU696 3.6 61.8 1.0
C A:ALA33 3.7 22.3 1.0
CB A:ASP9 3.7 22.4 1.0
C A:ASP9 3.9 21.1 1.0
CB A:THR34 3.9 24.5 1.0
CA A:ALA33 3.9 16.9 1.0
O A:ASP8 4.0 21.7 1.0
CA A:THR34 4.1 17.6 1.0
N A:ALA33 4.2 17.5 1.0
CA A:ASP9 4.3 19.4 1.0
CG1 A:VAL101 4.4 24.7 1.0
O A:ALA33 4.4 22.2 1.0
CG2 A:VAL101 4.5 26.1 1.0
CG A:GLU696 4.5 55.8 1.0
C A:ALA32 4.6 21.1 1.0
O A:ALA32 4.8 17.9 1.0
C A:ASP8 4.8 22.1 1.0
CB A:ALA32 4.9 20.8 1.0
N A:VAL10 4.9 18.4 1.0

Sodium binding site 8 out of 19 in 5cgm

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Sodium binding site 8 out of 19 in the Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na711

b:38.8
occ:1.00
 OD2 A:ASP498 2.7 33.5 1.0
HO3' A:MAL701 2.8 20.4 1.0
O A:HOH807 2.8 16.8 1.0
O3' A:MAL701 2.8 21.1 1.0
O2' A:MAL701 3.2 30.7 1.0
CH2 A:TRP300 3.2 18.9 1.0
CZ2 A:TRP300 3.4 17.6 1.0
H2' A:MAL701 3.4 33.1 1.0
CB A:PRO497 3.4 16.0 1.0
CG A:ASP498 3.4 32.0 1.0
CG A:PRO497 3.5 19.2 1.0
CD A:PRO497 3.5 15.2 1.0
OD1 A:ASP498 3.6 29.0 1.0
C2' A:MAL701 3.7 32.4 1.0
HO2' A:MAL701 3.8 31.3 1.0
C3' A:MAL701 3.8 27.6 1.0
CZ3 A:TRP300 4.0 18.8 1.0
CE2 A:TRP300 4.2 18.7 1.0
CD A:LYS552 4.2 20.0 1.0
H3' A:MAL701 4.2 27.4 1.0
O A:HOH808 4.3 38.2 1.0
N A:PRO497 4.3 15.5 1.0
CA A:PRO497 4.3 14.8 1.0
N A:ASP498 4.3 17.8 1.0
C A:PRO497 4.5 19.3 1.0
OE2 A:GLU231 4.5 22.9 1.0
O A:HOH834 4.5 26.8 1.0
CG A:LYS552 4.6 18.0 1.0
NH2 A:ARG411 4.6 22.8 1.0
CB A:ASP498 4.7 21.5 1.0
CE3 A:TRP300 4.8 16.5 1.0
CD2 A:TRP300 4.9 15.6 1.0
H1 A:MAL701 5.0 24.0 1.0

Sodium binding site 9 out of 19 in 5cgm

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Sodium binding site 9 out of 19 in the Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na712

b:47.4
occ:1.00
 O A:HOH1280 2.6 38.1 1.0
O A:ARG558 2.9 24.5 1.0
O A:HOH1014 2.9 21.2 1.0
N A:ARG558 3.0 18.7 1.0
O A:HOH1040 3.1 27.7 1.0
CE2 A:PHE560 3.6 23.9 1.0
C A:ARG558 3.7 24.9 1.0
O A:SER236 3.7 21.5 1.0
CA A:ARG558 3.8 19.6 1.0
O A:HOH1093 3.9 51.6 1.0
CB A:ARG558 3.9 20.0 1.0
C A:PRO557 4.0 22.0 1.0
O A:HOH1236 4.0 61.4 1.0
CA A:PRO557 4.0 18.6 1.0
CD2 A:PHE560 4.1 21.2 1.0
CL A:CL715 4.3 51.9 1.0
O A:HOH1281 4.5 44.0 1.0
CZ A:PHE560 4.5 22.1 1.0
O A:HOH1279 4.7 34.1 1.0
CG A:ARG558 4.8 19.4 1.0
CB A:PRO557 4.8 20.5 1.0
CA A:THR237 4.8 16.5 1.0
C A:SER236 4.8 20.6 1.0
O A:ARG556 4.8 20.4 1.0
N A:ASP559 5.0 23.2 1.0

Sodium binding site 10 out of 19 in 5cgm

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Sodium binding site 10 out of 19 in the Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of Mycobacterium Thermoresistibile Glge in Complex with Maltose at 1.95A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na713

b:22.1
occ:1.00
 OH5 A:1PE716 2.4 22.6 1.0
O A:HOH964 2.4 22.7 1.0
OH6 A:1PE716 2.4 34.8 1.0
OH4 A:1PE716 2.5 27.9 1.0
OH2 A:1PE716 2.6 34.2 1.0
OH3 A:1PE716 2.6 27.4 1.0
C14 A:1PE716 3.3 20.9 1.0
C25 A:1PE716 3.3 24.0 1.0
C24 A:1PE716 3.3 23.9 1.0
C15 A:1PE716 3.4 27.6 1.0
C13 A:1PE716 3.4 26.3 1.0
C26 A:1PE716 3.5 43.2 1.0
C23 A:1PE716 3.5 27.0 1.0
C12 A:1PE716 3.5 32.5 1.0
C22 A:1PE716 3.5 26.6 1.0
OH7 A:1PE716 3.7 54.3 1.0
C16 A:1PE716 3.8 49.8 1.0
O A:GLU353 4.5 23.8 1.0
O A:HOH1261 4.9 56.4 1.0

Reference:

V.Mendes, M.Blaszczyk, A.Maranha, N.Empadinhas, T.L.Blundell. Structure of Mycobacterium Thermoresistibile Glge Defines Novel Conformational States That Contribute to the Catalytic Mechanism. Sci Rep V. 5 17144 2015.
ISSN: ESSN 2045-2322
PubMed: 26616850
DOI: 10.1038/SREP17144
Page generated: Mon Oct 7 20:19:56 2024

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