Atomistry » Manganese » PDB 6q9p-6qv8 » 6qru
Atomistry »
  Manganese »
    PDB 6q9p-6qv8 »
      6qru »

Manganese in PDB 6qru: X-Ray Radiation Dose Series on Xylose Isomerase - 2.01 Mgy

Enzymatic activity of X-Ray Radiation Dose Series on Xylose Isomerase - 2.01 Mgy

All present enzymatic activity of X-Ray Radiation Dose Series on Xylose Isomerase - 2.01 Mgy:
5.3.1.5;

Protein crystallography data

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 2.01 Mgy, PDB code: 6qru was solved by H.Taberman, C.S.Bury, M.J.Van Der Woerd, E.H.Snell, E.F.Garman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.26 / 1.17
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.542, 97.544, 102.537, 90.00, 90.00, 90.00
R / Rfree (%) 10.1 / 11.9

Other elements in 6qru:

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 2.01 Mgy also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Radiation Dose Series on Xylose Isomerase - 2.01 Mgy (pdb code 6qru). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the X-Ray Radiation Dose Series on Xylose Isomerase - 2.01 Mgy, PDB code: 6qru:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6qru

Go back to Manganese Binding Sites List in 6qru
Manganese binding site 1 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 2.01 Mgy


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Radiation Dose Series on Xylose Isomerase - 2.01 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn414

b:9.9
occ:0.41
MN A:MN414 0.0 9.9 0.4
MN A:MN414 0.8 10.2 0.5
OD1 A:ASP257 1.7 12.8 0.7
MN A:MN414 1.7 9.3 0.1
OD1 A:ASP257 1.8 10.6 0.3
OD2 A:ASP255 1.9 12.5 0.4
O A:HOH568 1.9 15.6 1.0
OE2 A:GLU217 2.0 9.8 0.9
OE2 A:GLU217 2.1 8.0 0.1
OD2 A:ASP255 2.6 12.0 0.6
CG A:ASP257 2.6 12.8 0.7
OD1 A:ASP255 2.6 9.7 0.6
CG A:ASP257 2.7 10.5 0.3
CG A:ASP255 2.8 12.1 0.4
OD2 A:ASP257 2.9 14.6 0.7
OD1 A:ASP255 2.9 13.4 0.4
CG A:ASP255 2.9 10.3 0.6
OD2 A:ASP257 3.0 10.6 0.3
CD A:GLU217 3.0 9.6 0.9
NE2 A:HIS220 3.0 10.1 0.7
HD21 A:ASN247 3.2 11.4 1.0
OE1 A:GLU217 3.3 11.0 0.9
CD A:GLU217 3.3 8.1 0.1
HD22 A:ASN247 3.5 11.4 1.0
NE2 A:HIS220 3.6 8.6 0.3
HD2 A:HIS220 3.6 9.8 0.3
O A:HOH548 3.7 60.0 0.5
ND2 A:ASN247 3.7 9.5 1.0
CD2 A:HIS220 3.7 9.7 0.7
O A:HOH536 3.8 32.7 1.0
HD2 A:HIS220 3.8 11.7 0.7
OE1 A:GLU217 3.9 8.2 0.1
CD2 A:HIS220 3.9 8.2 0.3
CE1 A:HIS220 3.9 10.0 0.7
O A:HOH629 4.0 16.9 0.7
CB A:ASP257 4.1 11.5 0.7
HE1 A:HIS220 4.1 11.9 0.7
CB A:ASP257 4.1 10.0 0.3
O A:HOH525 4.1 12.1 1.0
HA A:ASP257 4.2 11.1 0.3
HA A:ASP257 4.2 11.7 0.7
CB A:ASP255 4.2 10.7 0.4
O A:HOH584 4.3 76.3 0.9
HG2 A:GLU217 4.3 9.5 0.1
OD2 A:ASP287 4.3 12.1 1.0
O A:HOH520 4.3 27.0 0.9
CG A:GLU217 4.4 9.0 0.9
HB3 A:ASP255 4.4 12.8 0.4
H A:ASP257 4.4 10.8 0.3
H A:ASP257 4.4 10.8 0.7
HG2 A:GLU217 4.4 10.8 0.9
CB A:ASP255 4.4 10.0 0.6
CG A:GLU217 4.5 7.9 0.1
HB3 A:ASP257 4.5 12.0 0.3
HB2 A:ASP257 4.5 13.8 0.7
O A:ASP287 4.5 10.2 1.0
CA A:ASP257 4.6 9.7 0.7
CA A:ASP257 4.6 9.3 0.3
HE3 A:LYS183 4.6 12.4 0.3
HB3 A:ASP257 4.6 13.8 0.7
CG A:ASP287 4.6 10.1 1.0
HB2 A:ASP255 4.6 12.8 0.4
HZ2 A:LYS183 4.7 13.5 0.3
HZ2 A:LYS289 4.7 17.7 0.7
HB2 A:ASP257 4.7 12.0 0.3
N A:ASP257 4.7 9.0 1.0
CE1 A:HIS220 4.7 8.4 0.3
HB3 A:ASP255 4.8 12.0 0.6
MG A:MG416 4.8 7.0 0.6
HG3 A:GLU217 4.8 10.8 0.9
HE3 A:LYS183 4.8 13.5 0.7
HZ3 A:LYS289 4.8 17.7 0.7
OD1 A:ASP287 4.8 10.4 1.0
HZ1 A:LYS183 4.8 13.5 0.3
CG A:HIS220 4.9 8.7 0.7
HB3 A:ASP287 4.9 11.3 1.0
HB2 A:ASP255 4.9 12.0 0.6
ND1 A:HIS220 4.9 9.5 0.7
CG A:ASN247 5.0 8.2 1.0
MN A:MN415 5.0 19.6 0.5

Manganese binding site 2 out of 4 in 6qru

Go back to Manganese Binding Sites List in 6qru
Manganese binding site 2 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 2.01 Mgy


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Radiation Dose Series on Xylose Isomerase - 2.01 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn414

b:10.2
occ:0.54
MN A:MN414 0.0 10.2 0.5
MN A:MN414 0.8 9.9 0.4
MN A:MN414 1.3 9.3 0.1
OD2 A:ASP255 1.6 12.5 0.4
OE2 A:GLU217 2.0 9.8 0.9
OE2 A:GLU217 2.2 8.0 0.1
OD2 A:ASP255 2.2 12.0 0.6
NE2 A:HIS220 2.2 10.1 0.7
OD1 A:ASP255 2.3 9.7 0.6
O A:HOH568 2.3 15.6 1.0
OD1 A:ASP257 2.4 12.8 0.7
CG A:ASP255 2.4 12.1 0.4
OD1 A:ASP257 2.5 10.6 0.3
CG A:ASP255 2.6 10.3 0.6
OD1 A:ASP255 2.6 13.4 0.4
NE2 A:HIS220 2.9 8.6 0.3
HD2 A:HIS220 2.9 9.8 0.3
CD A:GLU217 2.9 9.6 0.9
CD2 A:HIS220 3.0 9.7 0.7
HD2 A:HIS220 3.1 11.7 0.7
CD2 A:HIS220 3.2 8.2 0.3
OE1 A:GLU217 3.3 11.0 0.9
CE1 A:HIS220 3.3 10.0 0.7
O A:HOH536 3.3 32.7 1.0
CG A:ASP257 3.3 12.8 0.7
CD A:GLU217 3.3 8.1 0.1
CG A:ASP257 3.4 10.5 0.3
HD21 A:ASN247 3.5 11.4 1.0
OD2 A:ASP257 3.5 10.6 0.3
HE1 A:HIS220 3.6 11.9 0.7
OD2 A:ASP257 3.6 14.6 0.7
O A:HOH548 3.8 60.0 0.5
O A:HOH629 3.8 16.9 0.7
HE3 A:LYS183 3.8 12.4 0.3
CB A:ASP255 3.9 10.7 0.4
OE1 A:GLU217 4.0 8.2 0.1
HE3 A:LYS183 4.0 13.5 0.7
HD22 A:ASN247 4.1 11.4 1.0
HZ2 A:LYS183 4.1 13.5 0.3
CB A:ASP255 4.1 10.0 0.6
O A:HOH584 4.1 76.3 0.9
CE1 A:HIS220 4.1 8.4 0.3
ND2 A:ASN247 4.1 9.5 1.0
HB3 A:ASP255 4.1 12.8 0.4
HB2 A:ASP255 4.1 12.8 0.4
CG A:HIS220 4.2 8.7 0.7
O A:HOH525 4.2 12.1 1.0
HG2 A:GLU217 4.3 9.5 0.1
CG A:GLU217 4.3 9.0 0.9
ND1 A:HIS220 4.3 9.5 0.7
HZ1 A:LYS183 4.3 13.5 0.3
HG2 A:GLU217 4.3 10.8 0.9
HB2 A:ASP255 4.4 12.0 0.6
CG A:GLU217 4.4 7.9 0.1
HB3 A:ASP255 4.5 12.0 0.6
NZ A:LYS183 4.5 11.3 0.3
CG A:HIS220 4.5 7.7 0.3
HZ2 A:LYS183 4.5 16.1 0.7
HE1 A:HIS220 4.5 10.1 0.3
O A:HOH520 4.6 27.0 0.9
CE A:LYS183 4.6 10.3 0.3
OD2 A:ASP287 4.7 12.1 1.0
HD2 A:LYS183 4.7 11.9 0.3
H A:ASP257 4.8 10.8 0.3
H A:ASP257 4.8 10.8 0.7
CB A:ASP257 4.8 11.5 0.7
HA A:ASP257 4.8 11.1 0.3
HA A:ASP257 4.8 11.7 0.7
MG A:MG416 4.8 7.0 0.6
HD2 A:LYS183 4.8 12.0 0.7
CB A:ASP257 4.8 10.0 0.3
HG3 A:GLU217 4.8 10.8 0.9
CE A:LYS183 4.9 11.3 0.7
ND1 A:HIS220 4.9 7.9 0.3
HA A:ASP255 4.9 11.2 1.0
HB3 A:GLU217 4.9 9.5 0.1
H A:HIS220 5.0 9.5 0.3
NZ A:LYS183 5.0 13.4 0.7
HZ1 A:LYS183 5.0 16.1 0.7

Manganese binding site 3 out of 4 in 6qru

Go back to Manganese Binding Sites List in 6qru
Manganese binding site 3 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 2.01 Mgy


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Radiation Dose Series on Xylose Isomerase - 2.01 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn414

b:9.3
occ:0.05
MN A:MN414 0.0 9.3 0.1
MN A:MN414 1.3 10.2 0.5
MN A:MN414 1.7 9.9 0.4
NE2 A:HIS220 1.8 10.1 0.7
O A:HOH568 2.0 15.6 1.0
NE2 A:HIS220 2.1 8.6 0.3
OE2 A:GLU217 2.3 8.0 0.1
OE2 A:GLU217 2.3 9.8 0.9
CE1 A:HIS220 2.3 10.0 0.7
HE1 A:HIS220 2.4 11.9 0.7
OD2 A:ASP255 2.5 12.5 0.4
OE1 A:GLU217 2.6 11.0 0.9
O A:HOH629 2.6 16.9 0.7
CD A:GLU217 2.7 9.6 0.9
O A:HOH536 2.8 32.7 1.0
OD2 A:ASP255 2.9 12.0 0.6
CD2 A:HIS220 2.9 8.2 0.3
CD2 A:HIS220 3.0 9.7 0.7
CD A:GLU217 3.0 8.1 0.1
HD2 A:HIS220 3.0 9.8 0.3
CE1 A:HIS220 3.1 8.4 0.3
O A:HOH584 3.1 76.3 0.9
OE1 A:GLU217 3.3 8.2 0.1
OD1 A:ASP255 3.4 9.7 0.6
HE1 A:HIS220 3.4 10.1 0.3
HD2 A:HIS220 3.4 11.7 0.7
OD1 A:ASP257 3.5 12.8 0.7
CG A:ASP255 3.5 12.1 0.4
CG A:ASP255 3.5 10.3 0.6
O A:HOH548 3.5 60.0 0.5
ND1 A:HIS220 3.5 9.5 0.7
OD1 A:ASP257 3.6 10.6 0.3
OD1 A:ASP255 3.8 13.4 0.4
MG A:MG416 3.8 7.0 0.6
HZ2 A:LYS183 3.8 13.5 0.3
HE3 A:LYS183 3.8 12.4 0.3
CG A:HIS220 3.8 8.7 0.7
OD2 A:ASP287 4.0 12.1 1.0
MN A:MN415 4.0 19.6 0.5
HD2 A:LYS183 4.0 11.9 0.3
CG A:HIS220 4.1 7.7 0.3
HE3 A:LYS183 4.1 13.5 0.7
ND1 A:HIS220 4.1 7.9 0.3
CG A:GLU217 4.1 9.0 0.9
HD2 A:LYS183 4.2 12.0 0.7
OD2 A:ASP257 4.2 14.6 0.7
HD21 A:ASN247 4.2 11.4 1.0
HD1 A:HIS220 4.2 11.4 0.7
CG A:GLU217 4.3 7.9 0.1
CG A:ASP257 4.3 12.8 0.7
OE2 A:GLU181 4.3 12.4 1.0
OD2 A:ASP257 4.3 10.6 0.3
HG2 A:GLU217 4.3 9.5 0.1
HZ2 A:LYS183 4.4 16.1 0.7
CG A:ASP257 4.4 10.5 0.3
HG2 A:GLU217 4.4 10.8 0.9
NZ A:LYS183 4.4 11.3 0.3
HZ1 A:LYS183 4.5 13.5 0.3
CE A:LYS183 4.5 10.3 0.3
HB3 A:GLU217 4.5 9.5 0.1
HB3 A:GLU217 4.6 10.1 0.9
HO2 A:EDO401 4.7 15.9 1.0
HG3 A:GLU217 4.7 10.8 0.9
CG A:ASP287 4.7 10.1 1.0
CD A:LYS183 4.7 9.9 0.3
HO1 A:EDO409 4.8 71.1 1.0
CE A:LYS183 4.8 11.3 0.7
CB A:ASP255 4.8 10.7 0.4
HD22 A:ASN247 4.8 11.4 1.0
HB2 A:GLU217 4.8 9.5 0.1
HB2 A:GLU217 4.8 10.1 0.9
CB A:GLU217 4.8 8.4 0.9
CB A:GLU217 4.8 7.9 0.1
ND2 A:ASN247 4.8 9.5 1.0
HB2 A:ASP255 4.8 12.8 0.4
CD A:LYS183 4.9 10.0 0.7
HD1 A:HIS220 4.9 9.5 0.3
HG3 A:LYS183 4.9 11.1 0.7
HB3 A:ASP255 4.9 12.8 0.4
CB A:ASP255 4.9 10.0 0.6
NZ A:LYS183 5.0 13.4 0.7
HG3 A:GLU217 5.0 9.5 0.1

Manganese binding site 4 out of 4 in 6qru

Go back to Manganese Binding Sites List in 6qru
Manganese binding site 4 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 2.01 Mgy


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Radiation Dose Series on Xylose Isomerase - 2.01 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn415

b:19.6
occ:0.50
MG A:MG416 0.3 7.0 0.6
HO2 A:EDO401 1.3 15.9 1.0
OE1 A:GLU217 1.8 8.2 0.1
OD2 A:ASP245 1.9 12.5 1.0
OD2 A:ASP287 2.0 12.1 1.0
O2 A:EDO401 2.0 13.3 1.0
OE2 A:GLU181 2.1 12.4 1.0
OE1 A:GLU217 2.3 11.0 0.9
O A:HOH629 2.4 16.9 0.7
CD A:GLU181 3.0 11.6 1.0
CD A:GLU217 3.1 8.1 0.1
CG A:ASP287 3.1 10.1 1.0
C2 A:EDO401 3.1 14.4 1.0
CG A:ASP245 3.1 11.0 1.0
OE1 A:GLU181 3.2 12.9 1.0
H22 A:EDO401 3.3 17.2 1.0
HB3 A:ASP287 3.4 11.3 1.0
H21 A:EDO401 3.4 17.2 1.0
HB2 A:ASP287 3.4 11.3 1.0
CB A:ASP287 3.5 9.4 1.0
CD A:GLU217 3.5 9.6 0.9
HB2 A:GLU217 3.6 10.1 0.9
HB2 A:GLU217 3.7 9.5 0.1
HB3 A:ASP245 3.7 12.1 1.0
O A:HOH747 3.7 15.8 0.9
HE1 A:HIS220 3.8 11.9 0.7
OE2 A:GLU217 3.8 8.0 0.1
CB A:ASP245 3.9 10.1 1.0
HB2 A:ASP245 3.9 12.1 1.0
MN A:MN414 4.0 9.3 0.1
OD1 A:ASP245 4.1 12.4 1.0
O A:HOH568 4.1 15.6 1.0
CG A:GLU217 4.1 7.9 0.1
OD1 A:ASP287 4.2 10.4 1.0
HE1 A:HIS220 4.2 10.1 0.3
HG3 A:GLU217 4.3 9.5 0.1
HD21 A:ASN215 4.3 14.0 1.0
CG A:GLU217 4.3 9.0 0.9
CB A:GLU217 4.3 8.4 0.9
CE1 A:HIS220 4.3 10.0 0.7
HG3 A:GLU217 4.4 10.8 0.9
HZ2 A:TRP16 4.4 12.8 1.0
CG A:GLU181 4.4 11.2 1.0
CB A:GLU217 4.4 7.9 0.1
C1 A:EDO401 4.4 14.7 1.0
OE2 A:GLU217 4.4 9.8 0.9
O A:HOH584 4.5 76.3 0.9
HD22 A:ASN215 4.5 14.0 1.0
CE1 A:HIS220 4.5 8.4 0.3
HG3 A:GLU181 4.6 13.4 1.0
H12 A:EDO401 4.6 17.7 1.0
HG2 A:GLU181 4.6 13.4 1.0
HB3 A:GLU217 4.7 10.1 0.9
ND2 A:ASN215 4.7 11.7 1.0
NE2 A:HIS220 4.7 8.6 0.3
H11 A:EDO401 4.8 17.7 1.0
HO1 A:EDO409 4.8 71.1 1.0
HB3 A:GLU217 4.8 9.5 0.1
NE2 A:HIS220 5.0 10.1 0.7
HG2 A:GLU217 5.0 9.5 0.1
MN A:MN414 5.0 9.9 0.4

Reference:

H.Taberman, C.S.Bury, M.J.Van Der Woerd, E.H.Snell, E.F.Garman. Structural Knowledge or X-Ray Damage? A Case Study on Xylose Isomerase Illustrating Both. J.Synchrotron Radiat. V. 26 931 2019.
ISSN: ESSN 1600-5775
PubMed: 31274415
DOI: 10.1107/S1600577519005599
Page generated: Sun Oct 6 06:02:19 2024

Last articles

W in 8QLN
W in 8RJA
V in 8WTN
Te in 8QLN
Re in 9GHX
Rb in 8Z5C
Ni in 9C0T
Ni in 9C0S
Ni in 9GP1
Ni in 9FYO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy