Atomistry » Manganese » PDB 3q7c-3rl4 » 3qxb
Atomistry »
  Manganese »
    PDB 3q7c-3rl4 »
      3qxb »

Manganese in PDB 3qxb: Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution, PDB code: 3qxb was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.68 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 76.188, 94.903, 173.197, 90.00, 93.04, 90.00
R / Rfree (%) 15 / 19.2

Other elements in 3qxb:

The structure of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution also contains other interesting chemical elements:

Iron (Fe) 8 atoms
Chlorine (Cl) 5 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution (pdb code 3qxb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution, PDB code: 3qxb:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3qxb

Go back to Manganese Binding Sites List in 3qxb
Manganese binding site 1 out of 8 in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:25.2
occ:0.34
 FE A:FE301 0.0 26.7 0.7
OE1 A:GLU267 2.1 27.5 1.0
OE2 A:GLU159 2.2 20.9 1.0
OD2 A:ASP194 2.2 26.5 1.0
ND1 A:HIS225 2.3 19.6 1.0
O A:HOH617 2.3 28.8 1.0
O A:HOH507 2.3 23.0 1.0
CD A:GLU267 3.1 29.0 1.0
CE1 A:HIS225 3.1 23.1 1.0
CD A:GLU159 3.1 20.7 1.0
CG A:ASP194 3.2 25.6 1.0
CG A:HIS225 3.3 22.2 1.0
OE1 A:GLU159 3.4 25.9 1.0
OE2 A:GLU267 3.4 31.6 1.0
CB A:ASP194 3.6 25.7 1.0
CB A:HIS225 3.7 22.9 1.0
CE1 A:HIS197 4.0 25.7 1.0
CE1 A:HIS236 4.0 23.3 1.0
MN A:MN303 4.1 31.4 0.5
FE A:FE304 4.1 31.1 0.2
NE2 A:HIS197 4.1 24.9 1.0
NE2 A:HIS225 4.3 21.2 1.0
O A:HOH1078 4.3 35.4 1.0
OD1 A:ASP194 4.4 28.7 1.0
CD2 A:HIS225 4.4 20.8 1.0
CG A:GLU267 4.4 25.1 1.0
CG A:GLU159 4.5 22.0 1.0
NE2 A:HIS236 4.7 24.7 1.0
CB A:GLU267 4.7 22.4 1.0
ND1 A:HIS197 4.8 23.6 1.0
CA A:ASP194 4.9 26.1 1.0
O A:HOH1043 4.9 37.9 1.0
ND1 A:HIS236 5.0 23.7 1.0

Manganese binding site 2 out of 8 in 3qxb

Go back to Manganese Binding Sites List in 3qxb
Manganese binding site 2 out of 8 in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:31.4
occ:0.50
 FE A:FE304 0.0 31.1 0.2
OD2 A:ASP234 2.0 27.4 1.0
NE2 A:HIS236 2.1 24.7 1.0
NE2 A:HIS197 2.2 24.9 1.0
O A:HOH507 2.3 23.0 1.0
O A:HOH1291 2.4 50.1 1.0
CE1 A:HIS236 2.8 23.3 1.0
CG A:ASP234 3.0 27.9 1.0
CD2 A:HIS197 3.1 25.4 1.0
CE1 A:HIS197 3.2 25.7 1.0
OD1 A:ASP234 3.3 24.6 1.0
CD2 A:HIS236 3.3 22.1 1.0
OD2 A:ASP194 3.8 26.5 1.0
O A:HOH1078 3.9 35.4 1.0
ND1 A:HIS236 4.0 23.7 1.0
MN A:MN302 4.1 25.2 0.3
FE A:FE301 4.1 26.7 0.7
ND1 A:HIS197 4.3 23.6 1.0
CG A:HIS197 4.3 24.0 1.0
NE2 A:GLN227 4.3 24.8 1.0
CG A:HIS236 4.3 24.4 1.0
CB A:ASP234 4.3 29.5 1.0
O B:HOH898 4.4 36.3 1.0
O A:HOH601 4.5 27.1 1.0
CG A:ASP194 4.6 25.6 1.0
OE1 A:GLU267 4.6 27.5 1.0
OE2 A:GLU159 4.8 20.9 1.0

Manganese binding site 3 out of 8 in 3qxb

Go back to Manganese Binding Sites List in 3qxb
Manganese binding site 3 out of 8 in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:22.4
occ:0.34
 FE B:FE301 0.0 23.0 0.7
OE2 B:GLU159 2.1 20.8 1.0
OD2 B:ASP194 2.1 20.6 1.0
OE1 B:GLU267 2.2 23.6 1.0
ND1 B:HIS225 2.2 16.4 1.0
O B:HOH468 2.3 21.9 1.0
O B:HOH495 2.4 23.1 1.0
CE1 B:HIS225 3.0 18.3 1.0
CD B:GLU159 3.1 22.7 1.0
CD B:GLU267 3.1 26.5 1.0
CG B:ASP194 3.2 20.4 1.0
CG B:HIS225 3.3 22.3 1.0
OE2 B:GLU267 3.4 31.7 1.0
OE1 B:GLU159 3.4 25.1 1.0
CB B:ASP194 3.6 18.4 1.0
CB B:HIS225 3.8 22.0 1.0
CE1 B:HIS236 3.9 23.5 1.0
CE1 B:HIS197 4.0 22.0 1.0
FE B:FE304 4.1 30.0 0.2
MN B:MN303 4.1 30.1 0.5
O B:HOH1234 4.1 41.8 1.0
NE2 B:HIS197 4.1 19.3 1.0
NE2 B:HIS225 4.2 21.4 1.0
OD1 B:ASP194 4.3 25.5 1.0
CD2 B:HIS225 4.4 19.3 1.0
CG B:GLU159 4.4 20.8 1.0
CG B:GLU267 4.5 23.1 1.0
NE2 B:HIS236 4.6 24.6 1.0
ND1 B:HIS197 4.8 20.4 1.0
CB B:GLU267 4.8 22.1 1.0
CA B:ASP194 4.9 20.1 1.0
CD2 B:HIS197 4.9 20.2 1.0
ND1 B:HIS236 5.0 23.2 1.0

Manganese binding site 4 out of 8 in 3qxb

Go back to Manganese Binding Sites List in 3qxb
Manganese binding site 4 out of 8 in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn303

b:30.1
occ:0.50
 FE B:FE304 0.0 30.0 0.2
OD2 B:ASP234 1.9 24.6 1.0
NE2 B:HIS197 2.2 19.3 1.0
NE2 B:HIS236 2.2 24.6 1.0
O B:HOH468 2.2 21.9 1.0
O B:HOH1118 2.5 34.8 1.0
CG B:ASP234 2.8 26.1 1.0
CE1 B:HIS236 3.0 23.5 1.0
OD1 B:ASP234 3.1 22.7 1.0
CE1 B:HIS197 3.1 22.0 1.0
CD2 B:HIS197 3.2 20.2 1.0
CD2 B:HIS236 3.4 23.3 1.0
O B:HOH1234 3.7 41.8 1.0
OD2 B:ASP194 3.8 20.6 1.0
FE B:FE301 4.1 23.0 0.7
MN B:MN302 4.1 22.4 0.3
CB B:ASP234 4.1 26.5 1.0
ND1 B:HIS236 4.2 23.2 1.0
ND1 B:HIS197 4.3 20.4 1.0
CG B:HIS197 4.3 21.0 1.0
NE2 B:GLN227 4.3 21.0 1.0
CG B:HIS236 4.4 22.5 1.0
O B:HOH703 4.4 26.8 1.0
O A:HOH1130 4.5 37.4 1.0
CG B:ASP194 4.6 20.4 1.0
OE1 B:GLU267 4.7 23.6 1.0
OE2 B:GLU159 4.8 20.8 1.0

Manganese binding site 5 out of 8 in 3qxb

Go back to Manganese Binding Sites List in 3qxb
Manganese binding site 5 out of 8 in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn302

b:23.8
occ:0.34
 FE C:FE301 0.0 23.0 0.7
OD2 C:ASP194 2.1 21.7 1.0
OE2 C:GLU159 2.1 20.9 1.0
OE1 C:GLU267 2.1 25.4 1.0
ND1 C:HIS225 2.2 16.2 1.0
O C:HOH718 2.3 24.7 1.0
O C:HOH684 2.5 26.8 1.0
CE1 C:HIS225 3.0 18.9 1.0
CD C:GLU159 3.1 22.8 1.0
CD C:GLU267 3.1 29.7 1.0
CG C:ASP194 3.2 24.1 1.0
CG C:HIS225 3.3 17.4 1.0
OE2 C:GLU267 3.5 33.1 1.0
OE1 C:GLU159 3.5 23.9 1.0
CB C:ASP194 3.6 21.3 1.0
CB C:HIS225 3.7 18.7 1.0
CE1 C:HIS236 3.9 20.6 1.0
CE1 C:HIS197 4.0 23.0 1.0
FE C:FE304 4.1 26.5 0.2
MN C:MN303 4.2 26.3 0.5
NE2 C:HIS225 4.2 17.1 1.0
O C:HOH1187 4.2 38.1 1.0
NE2 C:HIS197 4.2 20.0 1.0
OD1 C:ASP194 4.3 26.4 1.0
CD2 C:HIS225 4.3 15.3 1.0
CG C:GLU159 4.4 20.0 1.0
CG C:GLU267 4.5 22.8 1.0
NE2 C:HIS236 4.6 17.2 1.0
ND1 C:HIS197 4.7 19.4 1.0
CB C:GLU267 4.8 21.1 1.0
CA C:ASP194 4.8 21.0 1.0
CD2 C:LEU192 4.9 23.6 1.0
O C:HOH1245 5.0 43.6 1.0

Manganese binding site 6 out of 8 in 3qxb

Go back to Manganese Binding Sites List in 3qxb
Manganese binding site 6 out of 8 in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn303

b:26.3
occ:0.50
 FE C:FE304 0.0 26.5 0.2
OD2 C:ASP234 1.9 25.3 1.0
NE2 C:HIS197 2.1 20.0 1.0
NE2 C:HIS236 2.2 17.2 1.0
O C:HOH718 2.2 24.7 1.0
O C:HOH1224 2.8 43.8 1.0
CG C:ASP234 2.9 24.8 1.0
CE1 C:HIS236 3.0 20.6 1.0
CE1 C:HIS197 3.1 23.0 1.0
CD2 C:HIS197 3.1 20.3 1.0
OD1 C:ASP234 3.2 24.8 1.0
CD2 C:HIS236 3.3 21.5 1.0
OD2 C:ASP194 3.9 21.7 1.0
O C:HOH1187 4.0 38.1 1.0
MN C:MN302 4.2 23.8 0.3
FE C:FE301 4.2 23.0 0.7
ND1 C:HIS197 4.2 19.4 1.0
ND1 C:HIS236 4.2 19.8 1.0
CG C:HIS197 4.2 20.7 1.0
CB C:ASP234 4.3 24.1 1.0
NE2 C:GLN227 4.3 17.3 1.0
O D:HOH1128 4.3 33.7 1.0
CG C:HIS236 4.3 20.0 1.0
O C:HOH554 4.5 22.1 1.0
CG C:ASP194 4.5 24.1 1.0
OE1 C:GLU267 4.6 25.4 1.0
OE2 C:GLU159 4.8 20.9 1.0
OD1 C:ASP194 4.8 26.4 1.0

Manganese binding site 7 out of 8 in 3qxb

Go back to Manganese Binding Sites List in 3qxb
Manganese binding site 7 out of 8 in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn302

b:26.5
occ:0.34
 FE D:FE301 0.0 26.4 0.7
OE1 D:GLU267 2.2 28.8 1.0
OE2 D:GLU159 2.2 20.3 1.0
OD2 D:ASP194 2.2 22.9 1.0
O D:HOH655 2.3 26.8 1.0
ND1 D:HIS225 2.4 19.1 1.0
O D:HOH967 2.5 29.8 1.0
CD D:GLU159 3.1 21.2 1.0
CD D:GLU267 3.1 29.9 1.0
CE1 D:HIS225 3.2 22.7 1.0
CG D:ASP194 3.2 23.7 1.0
OE1 D:GLU159 3.3 24.4 1.0
OE2 D:GLU267 3.3 36.1 1.0
CG D:HIS225 3.4 22.5 1.0
CB D:ASP194 3.6 21.8 1.0
CB D:HIS225 3.8 23.4 1.0
CE1 D:HIS236 3.9 23.7 1.0
CE1 D:HIS197 4.0 21.6 1.0
NE2 D:HIS197 4.1 20.8 1.0
FE D:FE304 4.2 27.4 0.2
MN D:MN303 4.2 28.1 0.5
NE2 D:HIS225 4.3 21.1 1.0
OD1 D:ASP194 4.4 22.1 1.0
CG D:GLU159 4.4 21.2 1.0
CD2 D:HIS225 4.5 21.7 1.0
CG D:GLU267 4.5 25.7 1.0
O D:HOH1212 4.5 41.0 1.0
NE2 D:HIS236 4.5 27.2 1.0
O D:HOH1272 4.7 41.5 1.0
ND1 D:HIS197 4.7 23.9 1.0
CB D:GLU267 4.8 24.9 1.0
CA D:ASP194 4.9 24.2 1.0
CD2 D:LEU192 4.9 22.4 1.0
CD2 D:HIS197 5.0 24.1 1.0

Manganese binding site 8 out of 8 in 3qxb

Go back to Manganese Binding Sites List in 3qxb
Manganese binding site 8 out of 8 in the Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of A Putative Xylose Isomerase (YP_426450.1) From Rhodospirillum Rubrum Atcc 11170 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn303

b:28.1
occ:0.50
 FE D:FE304 0.0 27.4 0.2
OD2 D:ASP234 2.1 23.7 1.0
NE2 D:HIS197 2.2 20.8 1.0
NE2 D:HIS236 2.2 27.2 1.0
O D:HOH655 2.3 26.8 1.0
O D:HOH1237 2.7 43.5 1.0
O D:HOH1279 2.7 47.4 1.0
CG D:ASP234 2.9 26.8 1.0
CE1 D:HIS236 3.1 23.7 1.0
CD2 D:HIS197 3.1 24.1 1.0
OD1 D:ASP234 3.1 22.0 1.0
CE1 D:HIS197 3.2 21.6 1.0
CD2 D:HIS236 3.2 26.3 1.0
OD2 D:ASP194 3.8 22.9 1.0
O D:HOH1272 4.0 41.5 1.0
O D:HOH1212 4.1 41.0 1.0
NE2 D:GLN227 4.2 22.2 1.0
MN D:MN302 4.2 26.5 0.3
FE D:FE301 4.2 26.4 0.7
ND1 D:HIS236 4.2 25.2 1.0
CG D:HIS197 4.3 22.5 1.0
O D:HOH987 4.3 33.7 1.0
ND1 D:HIS197 4.3 23.9 1.0
CB D:ASP234 4.3 25.9 1.0
CG D:HIS236 4.3 24.8 1.0
O D:HOH746 4.4 27.3 1.0
CG D:ASP194 4.6 23.7 1.0
O D:HOH1308 4.7 49.1 1.0
OE1 D:GLU267 4.8 28.8 1.0
OE2 D:GLU159 4.9 20.3 1.0
OD1 D:ASP194 5.0 22.1 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Sat Oct 5 17:42:51 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy