Atomistry » Calcium » PDB 3gy6-3hii » 3hbv
Atomistry »
  Calcium »
    PDB 3gy6-3hii »
      3hbv »

Calcium in PDB 3hbv: Prtc Methionine Mutants: M226A in-House

Protein crystallography data

The structure of Prtc Methionine Mutants: M226A in-House, PDB code: 3hbv was solved by A.E.Oberholzer, M.Bumann, T.Hege, S.Russo, U.Baumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.35 / 1.95
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.961, 101.961, 123.222, 90.00, 90.00, 120.00
R / Rfree (%) 15.3 / 16.6

Other elements in 3hbv:

The structure of Prtc Methionine Mutants: M226A in-House also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Prtc Methionine Mutants: M226A in-House (pdb code 3hbv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Prtc Methionine Mutants: M226A in-House, PDB code: 3hbv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3hbv

Go back to Calcium Binding Sites List in 3hbv
Calcium binding site 1 out of 7 in the Prtc Methionine Mutants: M226A in-House


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Prtc Methionine Mutants: M226A in-House within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca480

b:17.1
occ:1.00
O P:GLY299 2.3 15.9 1.0
OD2 P:ASP302 2.4 17.1 1.0
O P:ARG265 2.4 16.4 1.0
O P:GLY267 2.4 16.4 1.0
OG P:SER269 2.5 16.7 1.0
OD2 P:ASP297 2.5 16.3 1.0
OD1 P:ASP297 2.5 16.4 1.0
CG P:ASP297 2.8 17.8 1.0
CG P:ASP302 3.1 18.0 1.0
OD1 P:ASP302 3.4 16.9 1.0
CB P:SER269 3.5 16.1 1.0
C P:ARG265 3.5 20.1 1.0
C P:GLY299 3.5 17.2 1.0
C P:GLY267 3.6 20.6 1.0
N P:SER269 3.8 17.9 1.0
N P:GLY267 4.0 18.8 1.0
C P:THR266 4.0 18.6 1.0
N P:GLY299 4.2 16.1 1.0
CA P:THR266 4.3 18.8 1.0
CB P:ARG265 4.3 15.9 1.0
CA P:SER269 4.3 15.8 1.0
O P:HOH936 4.3 16.4 1.0
N P:THR266 4.3 17.6 1.0
CA P:GLY300 4.3 16.7 1.0
CB P:ASP297 4.3 17.7 1.0
N P:GLY300 4.4 17.2 1.0
CA P:GLY267 4.4 18.8 1.0
CB P:ASP302 4.5 16.0 1.0
O P:THR266 4.5 20.1 1.0
CA P:GLY299 4.5 17.5 1.0
CA P:ARG265 4.5 18.6 1.0
N P:ASP268 4.6 17.4 1.0
C P:GLY300 4.6 20.4 1.0
C P:ASP268 4.6 20.6 1.0
CA P:ASP268 4.6 16.6 1.0
OH P:TYR271 4.8 17.2 1.0
O P:GLY300 4.8 15.7 1.0

Calcium binding site 2 out of 7 in 3hbv

Go back to Calcium Binding Sites List in 3hbv
Calcium binding site 2 out of 7 in the Prtc Methionine Mutants: M226A in-House


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Prtc Methionine Mutants: M226A in-House within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca481

b:18.1
occ:1.00
OD1 P:ASP302 2.4 16.9 1.0
O P:THR339 2.4 16.2 1.0
O P:GLY300 2.4 15.7 1.0
O P:HOH937 2.5 19.4 1.0
O P:HOH936 2.5 16.4 1.0
OE1 P:GLU341 2.5 17.7 1.0
OE2 P:GLU341 2.6 18.5 1.0
CD P:GLU341 2.9 20.8 1.0
CG P:ASP302 3.5 18.0 1.0
C P:GLY300 3.6 20.4 1.0
C P:THR339 3.6 17.2 1.0
N P:ASP302 4.2 14.2 1.0
N P:GLY300 4.3 17.2 1.0
CB P:ASP302 4.3 16.0 1.0
C P:GLY299 4.3 17.2 1.0
OD2 P:ASP302 4.3 17.1 1.0
CB P:THR339 4.4 19.0 1.0
CA P:THR301 4.4 17.9 1.0
O P:HOH492 4.4 20.1 1.0
N P:THR301 4.4 18.4 1.0
O P:GLY299 4.4 15.9 1.0
CG P:GLU341 4.4 17.1 1.0
OD1 P:ASP297 4.4 16.4 1.0
CA P:THR339 4.5 17.1 1.0
CA P:GLY300 4.5 16.7 1.0
N P:ILE340 4.5 14.9 1.0
CA P:ILE340 4.5 17.5 1.0
C P:THR301 4.7 17.5 1.0
CG2 P:THR339 4.8 20.1 1.0
N P:GLU341 4.8 14.7 1.0
N P:THR339 4.9 16.0 1.0
CA P:GLY299 4.9 17.5 1.0
CA P:ASP302 4.9 16.2 1.0

Calcium binding site 3 out of 7 in 3hbv

Go back to Calcium Binding Sites List in 3hbv
Calcium binding site 3 out of 7 in the Prtc Methionine Mutants: M226A in-House


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Prtc Methionine Mutants: M226A in-House within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca482

b:21.3
occ:1.00
O P:ALA365 2.4 22.8 1.0
O P:GLY346 2.4 22.1 1.0
O P:GLY363 2.4 19.3 1.0
OD2 P:ASP350 2.4 21.8 1.0
OD1 P:ASP368 2.4 20.6 1.0
O P:GLY348 2.5 20.1 1.0
OD2 P:ASP368 2.9 20.4 1.0
CG P:ASP368 3.0 21.9 1.0
CG P:ASP350 3.3 22.7 1.0
C P:GLY363 3.5 21.5 1.0
C P:GLY346 3.6 20.2 1.0
C P:ALA365 3.6 23.0 1.0
C P:GLY348 3.7 22.8 1.0
C P:GLY364 3.9 21.0 1.0
N P:GLY348 4.0 22.3 1.0
O P:GLY364 4.0 19.8 1.0
CB P:ASP350 4.1 21.4 1.0
N P:GLY346 4.1 18.6 1.0
C P:SER347 4.1 25.6 1.0
OD1 P:ASP350 4.1 23.3 1.0
N P:ALA365 4.2 22.0 1.0
N P:ASP350 4.2 20.6 1.0
CA P:GLY364 4.3 18.8 1.0
N P:GLY364 4.3 19.4 1.0
O P:HOH534 4.4 21.5 1.0
CA P:SER347 4.4 22.0 1.0
N P:SER347 4.4 20.4 1.0
CA P:GLY366 4.4 22.7 1.0
CA P:GLY348 4.4 24.1 1.0
CA P:GLY363 4.4 16.7 1.0
CB P:ASP368 4.4 18.1 1.0
CA P:GLY346 4.5 19.9 1.0
N P:GLY366 4.5 21.4 1.0
C P:GLY345 4.5 20.5 1.0
CA P:ALA365 4.6 21.6 1.0
O P:SER347 4.6 22.2 1.0
C P:GLY366 4.6 22.3 1.0
O P:GLY366 4.6 22.3 1.0
N P:ASN349 4.7 22.0 1.0
CA P:CA484 4.7 21.4 1.0
CA P:ASN349 4.8 19.5 1.0
CA P:ASP350 4.8 21.5 1.0
CA P:GLY345 4.8 16.4 1.0
C P:ASN349 4.9 24.4 1.0

Calcium binding site 4 out of 7 in 3hbv

Go back to Calcium Binding Sites List in 3hbv
Calcium binding site 4 out of 7 in the Prtc Methionine Mutants: M226A in-House


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Prtc Methionine Mutants: M226A in-House within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca483

b:18.8
occ:1.00
O P:ASN355 2.4 19.0 1.0
O P:GLY372 2.4 17.8 1.0
OD1 P:ASN359 2.4 19.3 1.0
O P:ALA374 2.4 18.1 1.0
O P:ALA357 2.4 17.7 1.0
OD1 P:ASP377 2.4 19.2 1.0
OD2 P:ASP377 3.0 17.4 1.0
CG P:ASP377 3.0 20.9 1.0
CG P:ASN359 3.4 20.1 1.0
C P:GLY372 3.5 19.9 1.0
C P:ASN355 3.6 20.0 1.0
C P:ALA374 3.6 20.4 1.0
C P:ALA357 3.7 20.5 1.0
N P:ASN355 4.0 19.5 1.0
C P:GLY373 4.0 20.5 1.0
C P:SER356 4.1 20.4 1.0
N P:ALA357 4.1 19.0 1.0
O P:GLY373 4.2 18.4 1.0
N P:ASN359 4.2 18.3 1.0
CB P:ASN359 4.2 16.6 1.0
N P:ALA374 4.2 18.6 1.0
ND2 P:ASN359 4.3 18.6 1.0
CA P:GLY372 4.3 18.6 1.0
N P:GLY373 4.4 21.0 1.0
CA P:SER356 4.4 19.9 1.0
CA P:GLY373 4.4 19.1 1.0
O P:SER356 4.4 21.6 1.0
CA P:GLY375 4.4 19.8 1.0
N P:SER356 4.4 17.6 1.0
CA P:ASN355 4.4 19.3 1.0
N P:GLY375 4.5 18.3 1.0
CB P:ASP377 4.5 16.1 1.0
OD1 P:ASN355 4.5 19.4 1.0
CA P:ALA357 4.5 21.8 1.0
CA P:ALA374 4.6 18.7 1.0
N P:ASP358 4.6 15.6 1.0
CA P:CA487 4.6 19.5 1.0
CA P:ASP358 4.6 20.3 1.0
C P:GLY354 4.6 20.5 1.0
C P:GLY375 4.7 20.4 1.0
O P:GLY375 4.7 16.8 1.0
C P:ASP358 4.8 21.9 1.0
CA P:GLY354 4.8 14.6 1.0
CA P:ASN359 4.8 15.2 1.0

Calcium binding site 5 out of 7 in 3hbv

Go back to Calcium Binding Sites List in 3hbv
Calcium binding site 5 out of 7 in the Prtc Methionine Mutants: M226A in-House


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Prtc Methionine Mutants: M226A in-House within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca484

b:21.4
occ:1.00
OD2 P:ASP368 2.4 20.4 1.0
O P:GLY364 2.4 19.8 1.0
OD1 P:ASP386 2.4 22.9 1.0
O P:ALA383 2.4 23.2 1.0
O P:GLY381 2.4 18.5 1.0
O P:GLY366 2.4 22.3 1.0
OD2 P:ASP386 2.9 24.1 1.0
CG P:ASP386 3.0 25.0 1.0
CG P:ASP368 3.5 21.9 1.0
C P:GLY381 3.5 21.7 1.0
C P:GLY364 3.6 21.0 1.0
C P:ALA383 3.6 25.0 1.0
C P:GLY366 3.6 22.3 1.0
C P:ALA365 3.8 23.0 1.0
O P:ALA365 3.8 22.8 1.0
C P:GLY382 3.8 23.0 1.0
O P:GLY382 3.9 21.2 1.0
CB P:ASP368 4.1 18.1 1.0
CA P:GLY382 4.1 19.1 1.0
N P:GLY366 4.1 21.4 1.0
N P:ASP368 4.1 19.9 1.0
CA P:ALA365 4.2 21.6 1.0
N P:ALA383 4.2 20.7 1.0
N P:GLY382 4.2 19.4 1.0
N P:ALA365 4.3 22.0 1.0
C P:GLY363 4.3 21.5 1.0
CA P:GLY384 4.4 26.0 1.0
N P:GLY384 4.4 25.6 1.0
N P:GLY364 4.4 19.4 1.0
CA P:GLY366 4.4 22.7 1.0
CB P:ASP386 4.5 22.0 1.0
OD1 P:ASP368 4.5 20.6 1.0
N P:ASN367 4.5 22.3 1.0
CA P:ALA383 4.6 21.6 1.0
CA P:GLY381 4.6 19.0 1.0
O P:GLY363 4.6 19.3 1.0
CA P:ASN367 4.6 20.2 1.0
CA P:GLY363 4.7 16.7 1.0
CA P:GLY364 4.7 18.8 1.0
C P:GLY384 4.7 26.1 1.0
CA P:CA482 4.7 21.3 1.0
CA P:CA485 4.7 20.9 0.8
CA P:ASP368 4.8 19.8 1.0
O P:GLY384 4.8 21.4 1.0
C P:ASN367 4.9 22.7 1.0

Calcium binding site 6 out of 7 in 3hbv

Go back to Calcium Binding Sites List in 3hbv
Calcium binding site 6 out of 7 in the Prtc Methionine Mutants: M226A in-House


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Prtc Methionine Mutants: M226A in-House within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca485

b:20.9
occ:0.80
OD2 P:ASP386 2.3 24.1 1.0
OE1 P:GLN408 2.4 24.7 1.0
O P:GLY384 2.4 21.4 1.0
O P:GLY382 2.4 21.2 1.0
O P:HOH12 2.5 19.8 1.0
OD1 P:ASP412 2.5 22.7 1.0
CG P:ASP412 3.3 22.4 1.0
CG P:ASP386 3.4 25.0 1.0
OD2 P:ASP412 3.4 23.5 1.0
C P:GLY384 3.5 26.1 1.0
CD P:GLN408 3.5 28.6 1.0
C P:GLY382 3.7 23.0 1.0
N P:GLY384 3.9 25.6 1.0
C P:ALA383 3.9 25.0 1.0
CB P:ASP386 3.9 22.0 1.0
N P:ASP386 4.1 22.9 1.0
O P:ALA383 4.1 23.2 1.0
C P:GLY381 4.2 21.7 1.0
CA P:GLY384 4.2 26.0 1.0
N P:GLY382 4.3 19.4 1.0
CG P:GLN408 4.3 26.1 1.0
CA P:ALA383 4.4 21.6 1.0
OD1 P:ASP386 4.4 22.9 1.0
O P:GLY381 4.5 18.5 1.0
N P:ALA383 4.5 20.7 1.0
CA P:GLY381 4.5 19.0 1.0
N P:ARG385 4.5 23.2 1.0
NE2 P:GLN408 4.6 23.4 1.0
CA P:GLY382 4.6 19.1 1.0
CA P:ASP386 4.7 23.2 1.0
CB P:GLN408 4.7 23.7 1.0
CA P:CA484 4.7 21.4 1.0
CA P:ARG385 4.8 22.7 1.0
CG2 P:ILE411 4.8 27.4 1.0
CB P:ASP412 4.8 22.7 1.0
C P:ARG385 4.9 23.7 1.0

Calcium binding site 7 out of 7 in 3hbv

Go back to Calcium Binding Sites List in 3hbv
Calcium binding site 7 out of 7 in the Prtc Methionine Mutants: M226A in-House


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Prtc Methionine Mutants: M226A in-House within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca487

b:19.5
occ:1.00
OD2 P:ASP377 2.3 17.4 1.0
O P:ASP395 2.4 20.3 1.0
O P:GLY373 2.4 18.4 1.0
O P:GLY375 2.4 16.8 1.0
OD1 P:ASP402 2.5 19.5 1.0
O P:HOH938 2.5 17.2 1.0
CG P:ASP402 3.4 20.5 1.0
CG P:ASP377 3.4 20.9 1.0
C P:ASP395 3.5 21.7 1.0
C P:GLY375 3.5 20.4 1.0
C P:GLY373 3.6 20.5 1.0
OD2 P:ASP402 3.6 18.9 1.0
C P:ALA374 3.8 20.4 1.0
O P:ALA374 3.8 18.1 1.0
N P:GLY375 4.1 18.3 1.0
CB P:ASP377 4.1 16.1 1.0
N P:ASP377 4.1 16.3 1.0
C P:GLY372 4.1 19.9 1.0
CA P:ASP395 4.2 20.3 1.0
N P:GLY373 4.2 21.0 1.0
CA P:ALA374 4.3 18.7 1.0
OD1 P:ASP377 4.3 19.2 1.0
CA P:GLY375 4.4 19.8 1.0
O P:GLY372 4.4 17.8 1.0
N P:ALA374 4.4 18.6 1.0
CB P:ASP395 4.4 20.7 1.0
CA P:GLY372 4.5 18.6 1.0
N P:ALA376 4.5 16.3 1.0
CA P:GLY373 4.5 19.1 1.0
N P:SER396 4.5 18.1 1.0
CA P:CA483 4.6 18.8 1.0
CA P:ALA376 4.7 16.8 1.0
CA P:SER396 4.7 16.1 1.0
CB P:ASP402 4.7 17.1 1.0
O P:HOH6 4.7 18.6 1.0
CA P:ASP377 4.7 16.8 1.0
C P:ALA376 4.8 18.1 1.0
CB P:SER396 4.9 19.2 1.0

Reference:

A.E.Oberholzer, M.Bumann, T.Hege, S.Russo, U.Baumann. Metzincin'S Canonical Methionine Is Responsible For the Structural Integrity of the Zinc-Binding Site Biol.Chem. V. 390 875 2009.
ISSN: ISSN 1431-6730
PubMed: 19558324
DOI: 10.1515/BC.2009.100
Page generated: Sat Jul 13 10:55:10 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy