Atomistry » Magnesium » PDB 5t3k-5tfc » 5t4y
Atomistry »
  Magnesium »
    PDB 5t3k-5tfc »
      5t4y »

Magnesium in PDB 5t4y: Crystal Structure of BT1762-1763

Protein crystallography data

The structure of Crystal Structure of BT1762-1763, PDB code: 5t4y was solved by B.Van Den Berg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 130.35 / 3.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 110.826, 152.085, 253.005, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 27

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of BT1762-1763 (pdb code 5t4y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of BT1762-1763, PDB code: 5t4y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5t4y

Go back to Magnesium Binding Sites List in 5t4y
Magnesium binding site 1 out of 5 in the Crystal Structure of BT1762-1763


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of BT1762-1763 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:28.4
occ:1.00
 OD1 D:ASN664 1.9 75.9 1.0
O A:TYR273 2.0 70.1 1.0
OD1 A:ASN401 2.2 73.3 1.0
OE2 A:GLU262 2.5 64.7 1.0
OE1 A:GLU262 2.6 76.9 1.0
O A:SER399 2.7 55.5 1.0
CD A:GLU262 2.9 68.0 1.0
CG D:ASN664 3.1 58.4 1.0
C A:TYR273 3.2 66.4 1.0
CG A:ASN401 3.3 64.8 1.0
N A:TYR273 3.9 55.7 1.0
C A:SER399 3.9 70.5 1.0
ND2 A:ASN401 4.0 58.5 1.0
CA A:TYR273 4.0 54.8 1.0
ND2 D:ASN664 4.1 61.1 1.0
CB D:ASN664 4.1 46.2 1.0
N A:SER274 4.2 65.2 1.0
CA D:ASN664 4.2 53.5 1.0
C A:GLN272 4.2 62.4 1.0
OE1 A:GLN272 4.3 74.1 1.0
CA A:SER274 4.4 60.0 1.0
N A:ASN401 4.4 58.0 1.0
CG A:GLU262 4.4 61.8 1.0
CB A:SER399 4.4 53.5 1.0
CB A:TYR273 4.5 55.0 1.0
CB A:ASN401 4.5 69.3 1.0
CA A:GLN272 4.6 67.3 1.0
CA A:ASN401 4.6 58.5 1.0
CA A:SER399 4.7 54.0 1.0
O A:GLN272 4.7 71.1 1.0
N D:ASN664 4.8 56.5 1.0
OD2 D:ASP659 4.8 0.4 1.0
C A:LEU400 4.9 85.7 1.0
N A:LEU400 5.0 55.8 1.0

Magnesium binding site 2 out of 5 in 5t4y

Go back to Magnesium Binding Sites List in 5t4y
Magnesium binding site 2 out of 5 in the Crystal Structure of BT1762-1763


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of BT1762-1763 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:84.5
occ:1.00
 OH A:TYR519 1.9 0.3 1.0
O A:SER55 2.3 73.6 1.0
O A:VAL53 2.8 95.9 1.0
CZ A:TYR519 3.0 91.5 1.0
O A:CYS58 3.1 74.3 1.0
C A:SER55 3.4 88.5 1.0
CE1 A:TYR519 3.4 86.6 1.0
O A:ARG54 3.5 87.1 1.0
CE2 A:TYR508 3.6 85.3 1.0
C A:VAL53 3.7 92.9 1.0
C A:ARG54 3.7 87.8 1.0
CG A:GLU75 3.8 84.4 1.0
OH A:TYR508 4.0 99.0 1.0
N A:SER55 4.0 81.5 1.0
O A:GLU75 4.2 0.6 1.0
CE2 A:TYR519 4.2 73.5 1.0
OE2 A:GLU75 4.2 95.9 1.0
CZ A:TYR508 4.2 93.9 1.0
N A:ASP56 4.3 89.9 1.0
CA A:SER55 4.3 81.3 1.0
C A:CYS58 4.3 77.3 1.0
CA A:ARG54 4.4 85.8 1.0
CA A:ASP56 4.4 87.8 1.0
N A:ARG54 4.5 90.7 1.0
CD A:GLU75 4.5 93.4 1.0
CA A:VAL53 4.5 89.4 1.0
CD2 A:TYR508 4.6 85.2 1.0
N A:CYS58 4.7 84.6 1.0
CD1 A:TYR519 4.8 81.3 1.0
C A:ASP56 4.9 84.4 1.0
CB A:GLU75 5.0 79.1 1.0

Magnesium binding site 3 out of 5 in 5t4y

Go back to Magnesium Binding Sites List in 5t4y
Magnesium binding site 3 out of 5 in the Crystal Structure of BT1762-1763


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of BT1762-1763 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:4.7
occ:1.00
 OD1 C:ASN664 2.0 54.7 1.0
OD1 B:ASN401 2.1 60.6 1.0
O B:TYR273 2.3 62.5 1.0
OE1 B:GLU262 2.4 68.8 1.0
OE2 B:GLU262 2.4 50.4 1.0
CD B:GLU262 2.7 58.8 1.0
O B:SER399 2.8 55.2 1.0
CG C:ASN664 3.2 43.9 1.0
CG B:ASN401 3.2 60.9 1.0
C B:TYR273 3.5 49.3 1.0
ND2 B:ASN401 3.9 59.1 1.0
CB C:ASN664 3.9 43.5 1.0
N B:TYR273 4.0 42.3 1.0
CA C:ASN664 4.0 51.2 1.0
C B:SER399 4.1 51.1 1.0
CG B:GLU262 4.1 53.1 1.0
N B:ASN401 4.1 42.8 1.0
ND2 C:ASN664 4.2 43.9 1.0
CA B:TYR273 4.2 47.6 1.0
OE1 B:GLN272 4.2 42.9 1.0
C B:GLN272 4.3 53.4 1.0
CB B:ASN401 4.3 55.4 1.0
CA B:ASN401 4.4 42.8 1.0
CA B:GLN272 4.5 49.7 1.0
N B:SER274 4.5 43.5 1.0
N C:ASN664 4.5 55.7 1.0
CB B:TYR273 4.6 40.4 1.0
CB B:SER399 4.6 45.4 1.0
CA B:SER274 4.7 40.3 1.0
O B:GLN272 4.8 64.7 1.0
C B:LEU400 4.8 55.2 1.0
OD2 C:ASP659 4.8 61.3 1.0
CA B:SER399 4.9 42.1 1.0
CB B:GLU262 4.9 56.3 1.0

Magnesium binding site 4 out of 5 in 5t4y

Go back to Magnesium Binding Sites List in 5t4y
Magnesium binding site 4 out of 5 in the Crystal Structure of BT1762-1763


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of BT1762-1763 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:0.3
occ:1.00
 O B:VAL53 2.2 60.9 1.0
O B:SER55 2.2 53.1 1.0
OH B:TYR519 2.3 57.2 1.0
C B:SER55 3.3 68.9 1.0
O B:CYS58 3.3 59.1 1.0
CZ B:TYR519 3.4 66.4 1.0
C B:VAL53 3.4 57.4 1.0
CE2 B:TYR508 3.4 74.3 1.0
C B:ARG54 3.5 61.0 1.0
O B:ARG54 3.6 60.0 1.0
CE1 B:TYR519 3.6 71.0 1.0
N B:SER55 3.7 64.4 1.0
CG B:GLU75 3.8 86.0 1.0
OH B:TYR508 3.9 55.4 1.0
CA B:ARG54 4.0 57.2 1.0
CA B:SER55 4.1 66.2 1.0
N B:ARG54 4.1 54.3 1.0
CZ B:TYR508 4.2 56.2 1.0
N B:ASP56 4.3 79.4 1.0
O B:GLU75 4.3 78.7 1.0
CD2 B:TYR508 4.3 77.6 1.0
CA B:VAL53 4.4 58.2 1.0
CA B:ASP56 4.5 80.3 1.0
OE2 B:GLU75 4.5 0.0 1.0
C B:CYS58 4.5 60.2 1.0
CE2 B:TYR519 4.6 65.5 1.0
CD B:GLU75 4.7 0.0 1.0
CA B:GLU75 4.9 67.6 1.0
N B:CYS58 4.9 59.0 1.0
CB B:GLU75 4.9 69.5 1.0
C B:GLU75 5.0 75.3 1.0
C B:ASP56 5.0 84.8 1.0

Magnesium binding site 5 out of 5 in 5t4y

Go back to Magnesium Binding Sites List in 5t4y
Magnesium binding site 5 out of 5 in the Crystal Structure of BT1762-1763


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of BT1762-1763 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1101

b:47.8
occ:1.00
 O C:VAL843 2.1 0.6 1.0
OD1 C:ASP837 2.8 71.2 1.0
CB C:ASP839 2.8 82.5 1.0
OD1 C:ASN841 2.9 86.0 1.0
OD2 C:ASP839 2.9 99.0 1.0
C C:VAL843 3.1 0.2 1.0
CG C:ASP839 3.3 85.0 1.0
OD2 C:ASP848 3.5 0.6 1.0
CA C:ILE844 3.6 82.9 1.0
CG C:ASN841 3.7 83.5 1.0
N C:ILE844 3.7 0.1 1.0
N C:ASP845 3.7 79.4 1.0
ND2 C:ASN841 3.9 74.9 1.0
CB C:ASP848 3.9 0.2 1.0
CG C:ASP837 4.0 81.2 1.0
CG2 C:VAL843 4.1 0.5 1.0
CA C:ASP839 4.1 87.2 1.0
C C:ILE844 4.2 76.6 1.0
CG C:ASP848 4.2 0.8 1.0
N C:ASP839 4.3 81.8 1.0
CA C:VAL843 4.3 0.7 1.0
CA C:ASP848 4.5 84.5 1.0
OD1 C:ASP839 4.5 62.8 1.0
OD2 C:ASP845 4.5 0.7 1.0
N C:VAL843 4.5 0.2 1.0
CG C:ASP845 4.6 0.7 1.0
OD1 C:ASP845 4.7 0.9 1.0
CB C:ILE844 4.8 75.3 1.0
CB C:VAL843 4.8 0.3 1.0
OD2 C:ASP837 4.8 76.3 1.0
CG1 C:ILE844 4.8 78.1 1.0
CA C:ASP837 4.8 79.8 1.0
N C:ASP848 4.9 72.0 1.0
CA C:ASP845 4.9 89.1 1.0
CB C:ASP837 4.9 81.6 1.0

Reference:

A.J.Glenwright, K.R.Pothula, S.P.Bhamidimarri, D.S.Chorev, A.Basle, S.J.Firbank, H.Zheng, C.V.Robinson, M.Winterhalter, U.Kleinekathofer, D.N.Bolam, B.Van Den Berg. Structural Basis For Nutrient Acquisition By Dominant Members of the Human Gut Microbiota. Nature V. 541 407 2017.
ISSN: ESSN 1476-4687
PubMed: 28077872
DOI: 10.1038/NATURE20828
Page generated: Mon Sep 30 04:43:47 2024

Last articles

F in 4GCA
F in 4GE2
F in 4G9C
F in 4GAB
F in 4GA8
F in 4G90
F in 4G8R
F in 4G7G
F in 4G8O
F in 4G6O
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy